The following bug report has been submitted:
Platform: macOS-26.3.1-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: Aborted
Current thread 0x00000001f0467100 (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, PIL._imaging, chimerax.surface._surface, chimerax.map._map, openmm._openmm, openmm.app.internal.xtc_utils, openmm.app.internal.compiled, psutil._psutil_osx, psutil._psutil_posix, 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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group, kiwisolver._cext, chimerax.alignment_algs._sw, chimerax.alignment_algs._nw (total: 64)
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},
"logWritingSignature" : "ba8eb564385daa0cd4243ce662f2bf4fe72b83e5",
"bug_type" : "309",
"roots_installed" : 0,
"trmStatus" : 1,
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "67648e5334a82511f4acf879",
"factorPackIds" : [
],
"deploymentId" : 240000008
},
{
"rolloutId" : "67d07cd6a7affa169ae21f45",
"factorPackIds" : [
],
"deploymentId" : 240000002
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/amy/Desktop/SPA
> AAT_HNE/3C11_Fab_AAT_NE/3c11_aat_hen_csparc.cxs"
Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300,
pixel 0.867, shown at level 0.0665, step 2, values float32
Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at
level 0.0841, step 1, values float32
Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size
300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32
Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32
Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867,
shown at level 0.0503, step 2, values float32
Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel
0.867, shown at level 0.0806, step 1, values float32
Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size
128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32
Opened cryosparc_P371_J937_003_volume_map.mrc as #14, grid size 300,300,300,
pixel 0.867, shown at level 0.0245, step 2, values float32
Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #15, grid size
300,300,300, pixel 0.867, shown at level 0.0683, step 1, values float32
Opened cryosparc_P371_J948_003_volume_map.mrc as #21, grid size 300,300,300,
pixel 0.867, shown at level 0.0208, step 2, values float32
Opened cryosparc_P371_J948_003_volume_map.mrc z flip as #22, grid size
300,300,300, pixel 0.867, shown at level 0.0938, step 1, values float32
Opened J1122.mrc as #29, grid size 300,300,300, pixel 0.867, shown at level
0.071, step 2, values float32
Opened J1134.mrc as #34, grid size 300,300,300, pixel 0.867, shown at level
0.0707, step 2, values float32
Opened cryosparc_P483_molmap_of_combined_6A.mrc as #41, grid size 200,200,200,
pixel 1, shown at level 0.293, step 1, values float32
Opened AATHNEcombined map 6 as #8, grid size 43,51,63, pixel 2, shown at level
0.366, step 1, values float32
Opened copy of copy of AATHNEcombined map 6 as #45, grid size 43,51,63, pixel
2, shown at level 0.354, step 1, values float32
Log from Thu Mar 12 17:49:41 2026UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/amy/Desktop/SPA AAT_HNE/csparc.cxs"
Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300,
pixel 0.867, shown at level 0.0665, step 2, values float32
Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at
level 0.0841, step 1, values float32
Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size
300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32
Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32
Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867,
shown at level 0.0503, step 2, values float32
Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel
0.867, shown at level 0.0806, step 1, values float32
Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size
128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32
Opened cryosparc_P371_J937_003_volume_map.mrc as #14, grid size 300,300,300,
pixel 0.867, shown at level 0.0245, step 2, values float32
Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #15, grid size
300,300,300, pixel 0.867, shown at level 0.0683, step 1, values float32
Opened cryosparc_P371_J948_003_volume_map.mrc as #21, grid size 300,300,300,
pixel 0.867, shown at level 0.0208, step 2, values float32
Opened cryosparc_P371_J948_003_volume_map.mrc z flip as #22, grid size
300,300,300, pixel 0.867, shown at level 0.0938, step 1, values float32
Opened J1122.mrc as #29, grid size 300,300,300, pixel 0.867, shown at level
0.071, step 2, values float32
Opened J1134.mrc as #34, grid size 300,300,300, pixel 0.867, shown at level
0.0707, step 2, values float32
Log from Wed Feb 11 13:24:40 2026UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/amy/Desktop/3C11_Fab_AAT_NE/csparc.cxs
Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300,
pixel 0.867, shown at level 0.0665, step 2, values float32
Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at
level 0.0841, step 1, values float32
Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size
300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32
Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32
Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867,
shown at level 0.0503, step 2, values float32
Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel
0.867, shown at level 0.0806, step 1, values float32
Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size
128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32
Opened cryosparc_P371_J937_003_volume_map.mrc as #14, grid size 300,300,300,
pixel 0.867, shown at level 0.0245, step 2, values float32
Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #15, grid size
300,300,300, pixel 0.867, shown at level 0.0683, step 1, values float32
Opened cryosparc_P371_J948_003_volume_map.mrc as #21, grid size 300,300,300,
pixel 0.867, shown at level 0.0208, step 2, values float32
Opened cryosparc_P371_J948_003_volume_map.mrc z flip as #22, grid size
300,300,300, pixel 0.867, shown at level 0.0938, step 1, values float32
Opened J1122.mrc as #29, grid size 300,300,300, pixel 0.867, shown at level
0.071, step 2, values float32
Opened J1134.mrc as #34, grid size 300,300,300, pixel 0.867, shown at level
0.0707, step 2, values float32
Log from Sun Feb 1 23:24:08 2026UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/amy/Desktop/3C11_Fab_AAT_NE/csparc.cxs format session
Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300,
pixel 0.867, shown at level 0.0665, step 2, values float32
Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at
level 0.0841, step 1, values float32
Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size
300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32
Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32
Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867,
shown at level 0.0503, step 2, values float32
Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel
0.867, shown at level 0.0806, step 1, values float32
Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size
128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32
Opened cryosparc_P371_J937_003_volume_map.mrc as #14, grid size 300,300,300,
pixel 0.867, shown at level 0.0245, step 2, values float32
Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #15, grid size
300,300,300, pixel 0.867, shown at level 0.0683, step 1, values float32
Opened cryosparc_P371_J948_003_volume_map.mrc as #21, grid size 300,300,300,
pixel 0.867, shown at level 0.0208, step 2, values float32
Opened cryosparc_P371_J948_003_volume_map.mrc z flip as #22, grid size
300,300,300, pixel 0.867, shown at level 0.0938, step 1, values float32
Opened J1122.mrc as #29, grid size 300,300,300, pixel 0.867, shown at level
0.071, step 2, values float32
Opened J1134.mrc as #34, grid size 300,300,300, pixel 0.867, shown at level
0.0707, step 2, values float32
Log from Tue Jan 6 13:31:49 2026UCSF ChimeraX version: 1.9rc202411230619
(2024-11-23)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/apple/Downloads/csparc.cxs
Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300,
pixel 0.867, shown at level 0.0665, step 2, values float32
Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at
level 0.0841, step 1, values float32
Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size
300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32
Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32
Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867,
shown at level 0.0503, step 2, values float32
Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel
0.867, shown at level 0.0806, step 1, values float32
Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size
128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32
Opened cryosparc_P371_J937_003_volume_map.mrc as #14, grid size 300,300,300,
pixel 0.867, shown at level 0.0245, step 2, values float32
Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #15, grid size
300,300,300, pixel 0.867, shown at level 0.0683, step 1, values float32
Opened cryosparc_P371_J948_003_volume_map.mrc as #21, grid size 300,300,300,
pixel 0.867, shown at level 0.0208, step 2, values float32
Opened cryosparc_P371_J948_003_volume_map.mrc z flip as #22, grid size
300,300,300, pixel 0.867, shown at level 0.0938, step 1, values float32
Log from Wed Dec 31 02:28:23 2025UCSF ChimeraX version: 1.9rc202411230619
(2024-11-23)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/apple/Downloads/csparc.cxs
Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300,
pixel 0.867, shown at level 0.0665, step 2, values float32
Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at
level 0.0841, step 1, values float32
Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size
300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32
Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32
Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867,
shown at level 0.0503, step 2, values float32
Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel
0.867, shown at level 0.0806, step 1, values float32
Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size
128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32
Opened cryosparc_P371_J937_003_volume_map.mrc as #14, grid size 300,300,300,
pixel 0.867, shown at level 0.0245, step 2, values float32
Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #15, grid size
300,300,300, pixel 0.867, shown at level 0.0683, step 1, values float32
Opened cryosparc_P371_J948_003_volume_map.mrc as #21, grid size 300,300,300,
pixel 0.867, shown at level 0.0208, step 2, values float32
Opened cryosparc_P371_J948_003_volume_map.mrc z flip as #22, grid size
300,300,300, pixel 0.867, shown at level 0.0938, step 1, values float32
Log from Wed Dec 10 00:50:43 2025UCSF ChimeraX version: 1.9rc202411230619
(2024-11-23)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/apple/Downloads/csparc.cxs
Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300,
pixel 0.867, shown at level 0.0665, step 2, values float32
Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at
level 0.0841, step 1, values float32
Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size
300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32
Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32
Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867,
shown at level 0.0503, step 2, values float32
Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel
0.867, shown at level 0.0806, step 1, values float32
Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size
128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32
Log from Fri Nov 28 18:17:17 2025UCSF ChimeraX version: 1.9rc202411230619
(2024-11-23)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/apple/Downloads/csparc.cxs
Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300,
pixel 0.867, shown at level 0.0665, step 2, values float32
Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at
level 0.0841, step 1, values float32
Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size
300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32
Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32
Log from Tue Nov 25 15:20:48 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9rc202411230619 (2024-11-23)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 1ezx format mmcif fromDatabase pdb
1ezx title:
Crystal structure of A serpin:protease complex [more info...]
Chain information for 1ezx #1
---
Chain | Description | UniProt
A | ALPHA-1-ANTITRYPSIN | A1AT_HUMAN 24-358
B | ALPHA-1-ANTITRYPSIN | A1AT_HUMAN 359-394
C | TRYPSIN | TRY1_BOVIN 42-245
> open /Users/apple/Downloads/cryosparc_P371_J880_003_volume_map.mrc
Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300,
pixel 0.867, shown at level 0.0177, step 2, values float32
> volume #2 level 0.06652
> ui mousemode right "translate selected models"
> select add #1
3984 atoms, 3982 bonds, 5 pseudobonds, 592 residues, 3 models selected
> view matrix models #1,1,0,0,22.115,0,1,0,63.09,0,0,1,71.823
> view matrix models #1,1,0,0,69.177,0,1,0,79.741,0,0,1,64.119
> view matrix models #1,1,0,0,67.012,0,1,0,77.327,0,0,1,54.335
> view matrix models #1,1,0,0,68.613,0,1,0,71.318,0,0,1,51.449
> ui tool show "Fit in Map"
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 3984 atoms
average map value = 0.0438, steps = 92
shifted from previous position = 3.55
rotated from previous position = 4.42 degrees
atoms outside contour = 2880, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.99872483 -0.00989522 0.04950557 63.11308004
0.00699761 0.99827076 0.05836545 67.58136236
-0.04999751 -0.05794461 0.99706703 56.37622316
Axis -0.75528783 0.64614759 0.10969770
Axis point 0.00000000 1024.64866555 -1103.37084637
Rotation angle (degrees) 4.41598404
Shift along axis 2.18333524
> view matrix models
> #1,0.99872,-0.0098952,0.049506,62.468,0.0069976,0.99827,0.058365,78.039,-0.049998,-0.057945,0.99707,58.786
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.95028,-0.27274,-0.15028,221.56,0.30912,-0.88449,-0.34946,175.7,-0.037612,-0.37854,0.92482,78.268
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 3984 atoms
average map value = 0.04798, steps = 140
shifted from previous position = 7.9
rotated from previous position = 12.7 degrees
atoms outside contour = 2817, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
-0.90965137 -0.21420693 -0.35587888 224.37202412
0.34819532 -0.86039384 -0.37213231 169.35532345
-0.22648268 -0.46242602 0.85724429 105.26930309
Axis -0.15458157 -0.22152447 0.96282472
Axis point 107.00674340 114.53127832 0.00000000
Rotation angle (degrees) 163.01876555
Shift along axis 29.15575838
> view matrix models
> #1,-0.93537,-0.33888,0.10125,206.37,0.28885,-0.89713,-0.33425,173.15,0.2041,-0.2834,0.93703,61.97
> remove /C
Unknown command: remove /C
> delete /C
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 2975 atoms
average map value = 0.05683, steps = 168
shifted from previous position = 10.2
rotated from previous position = 20.9 degrees
atoms outside contour = 1876, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
-0.98775248 -0.03216686 0.15267718 185.97005837
0.01404291 -0.99287467 -0.11833294 193.09005228
0.15539570 -0.11473962 0.98116614 52.60294093
Axis 0.07739391 -0.05855237 0.99527976
Axis point 89.79478279 99.15188295 0.00000000
Rotation angle (degrees) 178.66978984
Shift along axis 55.44171271
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 2975 atoms
average map value = 0.05683, steps = 44
shifted from previous position = 0.00306
rotated from previous position = 0.00868 degrees
atoms outside contour = 1876, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
-0.98775300 -0.03230499 0.15264466 185.98147456
0.01419042 -0.99287622 -0.11830233 193.08167122
0.15537901 -0.11468739 0.98117489 52.59959002
Axis 0.07738151 -0.05853153 0.99528195
Axis point 89.79393478 99.15365724 0.00000000
Rotation angle (degrees) 178.66156873
Shift along axis 55.44158488
Deleted lines to meet Trac size limit. Tom
> hbonds #!39 reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 8pi2 #35/A ARG 101 NE
13841 hydrogen bonds found
> interfaces #!39 & ~solvent
5 buried areas: A C 2439, H L 1779, A H 684, A B 593, B L 433
> select #39/A:32@CB
1 atom, 1 residue, 1 model selected
> select clear
> select #39/H: 32
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #39/A: 32
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #39/H: 28
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel byhetero
> distance #39/A:32 #39/H:28
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 16 atoms and 0
measurable objects
> distance #39/A:32@OE1 #39/H:28@OG1
Distance between combined.pdb #39/A GLU 32 OE1 and /H THR 28 OG1: 3.567Å
> select up
48 atoms, 49 bonds, 5 residues, 1 model selected
> select up
1018 atoms, 1042 bonds, 134 residues, 1 model selected
> select down
48 atoms, 49 bonds, 5 residues, 1 model selected
> select down
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #39/A: 75
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #39/H: 56
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel byhetero
> distance #39/A:75@OE2 #39/H:56@OG
Distance between combined.pdb #39/A GLU 75 OE2 and /H SER 56 OG: 2.495Å
> select #39/A: 36
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #39/A: 306
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #39/A: 302
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #39/A: 2
Nothing selected
> select #39/A: 32
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #39/A: 36
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #39
7963 atoms, 7899 bonds, 1523 pseudobonds, 1256 residues, 4 models selected
> select subtract #39
Nothing selected
> select add #39
7963 atoms, 7899 bonds, 1523 pseudobonds, 1256 residues, 4 models selected
> show sel cartoons
> hide sel atoms
> hide sel cartoons
> show sel atoms
> hide sel cartoons
> hide sel atoms
> show sel cartoons
> ui tool show "Show Sequence Viewer"
> sequence chain #4/H #6/H #17/H #24/H #33/H #39/H
Alignment identifier is 1
> select clear
> select #4/H:1 #6/H:1 #17/H:1 #24/H:1 #33/H:1 #39/H:1
30 atoms, 24 bonds, 6 residues, 6 models selected
> select #4/H:1-169 #6/H:1-169 #17/H:1-169 #24/H:1-169 #33/H:1-169 #39/H:1-169
7686 atoms, 7878 bonds, 341 pseudobonds, 1020 residues, 13 models selected
Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-171] RMSD: 42.741
> select #4/H:213 #6/H:213 #17/H:213 #24/H:213 #33/H:213 #39/H:213
72 atoms, 66 bonds, 6 residues, 6 models selected
> select #4/H:151-213 #6/H:151-213 #17/H:151-213 #24/H:151-213 #33/H:151-213
> #39/H:151-213
2802 atoms, 2868 bonds, 149 pseudobonds, 378 residues, 7 models selected
Fab 3C11 Heavy Chain [ID: 1] region 6 chains [153-215] RMSD: 64.253
> select #4/H:1-2 #6/H:1-2 #17/H:1-2 #24/H:1-2 #33/H:1-2 #39/H:1-2
72 atoms, 66 bonds, 12 residues, 6 models selected
> select #4/H:1-146 #6/H:1-146 #17/H:1-146 #24/H:1-146 #33/H:1-146 #39/H:1-146
6678 atoms, 6828 bonds, 312 pseudobonds, 882 residues, 13 models selected
Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-148] RMSD: 40.342
> select #4/H:1 #6/H:1 #17/H:1 #24/H:1 #33/H:1 #39/H:1
30 atoms, 24 bonds, 6 residues, 6 models selected
> select #4/H:1-140 #6/H:1-140 #17/H:1-140 #24/H:1-140 #33/H:1-140 #39/H:1-140
6372 atoms, 6510 bonds, 303 pseudobonds, 846 residues, 13 models selected
Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-142] RMSD: 39.273
> select #4/H:1-2 #6/H:1-2 #17/H:1-2 #24/H:1-2 #33/H:1-2 #39/H:1-2
72 atoms, 66 bonds, 12 residues, 6 models selected
> select #4/H:1-132 #6/H:1-132 #17/H:1-132 #24/H:1-132 #33/H:1-132 #39/H:1-132
6108 atoms, 6252 bonds, 279 pseudobonds, 804 residues, 7 models selected
Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-134] RMSD: 36.760
> select #4/H:1 #6/H:1 #17/H:1 #24/H:1 #33/H:1 #39/H:1
30 atoms, 24 bonds, 6 residues, 6 models selected
> select #4/H:1-128 #6/H:1-128 #17/H:1-128 #24/H:1-128 #33/H:1-128 #39/H:1-128
5976 atoms, 6120 bonds, 277 pseudobonds, 780 residues, 7 models selected
Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-130] RMSD: 33.946
> select #4/H:1-2 #6/H:1-2 #17/H:1-2 #24/H:1-2 #33/H:1-2 #39/H:1-2
72 atoms, 66 bonds, 12 residues, 6 models selected
> select #4/H:1-94 #6/H:1-94 #17/H:1-94 #24/H:1-94 #33/H:1-94 #39/H:1-94
4548 atoms, 4644 bonds, 204 pseudobonds, 588 residues, 7 models selected
Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-98] RMSD: 25.989
> select #4/H:1-101 #6/H:1-101 #17/H:1-101 #24/H:1-101 #33/H:1-101 #39/H:1-101
4806 atoms, 4908 bonds, 222 pseudobonds, 618 residues, 7 models selected
Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-98] + 1 other block RMSD:
25.402
> select #4/H:1-106 #6/H:1-106 #17/H:1-106 #24/H:1-106 #33/H:1-106 #39/H:1-106
5058 atoms, 5178 bonds, 235 pseudobonds, 648 residues, 7 models selected
Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-98] + 2 other blocks RMSD:
25.227
> select #4/H:1-111 #6/H:1-111 #17/H:1-111 #24/H:1-111 #33/H:1-111 #39/H:1-111
5274 atoms, 5394 bonds, 258 pseudobonds, 678 residues, 7 models selected
Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-98] + 3 other blocks RMSD:
25.743
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #4/L #6/L #17/L #24/L #33/L #39/L
Alignment identifier is 1
> select #4/L:2 #6/L:2 #17/L:2 #24/L:2 #33/L:2 #39/L:2
48 atoms, 42 bonds, 6 residues, 6 models selected
> select #4/L:2-113 #6/L:2-113 #17/L:2-113 #24/L:2-113 #33/L:2-113 #39/L:2-113
4782 atoms, 4896 bonds, 292 pseudobonds, 636 residues, 13 models selected
Fab 3C11 Light Chain [ID: 1] region 6 chains [1-113] RMSD: 28.868
> select #4/L:2-113 #6/L:2-113 #17/L:2-113 #24/L:2-113 #33/L:2-113 #39/L:2-113
4782 atoms, 4896 bonds, 292 pseudobonds, 636 residues, 13 models selected
Fab 3C11 Light Chain [ID: 1] region 6 chains [1-113] + 1 other block RMSD:
30.988
> select clear
> select #4/L:2-97 #6/L:2-97 #17/L:2-97 #24/L:2-97 #33/L:2-97 #39/L:2-97
4128 atoms, 4236 bonds, 234 pseudobonds, 540 residues, 13 models selected
Fab 3C11 Light Chain [ID: 1] region 6 chains [1-97] RMSD: 25.885
> select #4/L:2-97,100-102 #6/L:2-97,100-102 #17/L:2-97,100-102
> #24/L:2-97,100-102 #33/L:2-97,100-102 #39/L:2-97,100-102
4200 atoms, 4302 bonds, 241 pseudobonds, 558 residues, 13 models selected
Fab 3C11 Light Chain [ID: 1] region 6 chains [1-97] + 1 other block RMSD:
25.843
> select #4/L:2-102 #6/L:2-102 #17/L:2-102 #24/L:2-102 #33/L:2-102 #39/L:2-102
4308 atoms, 4422 bonds, 261 pseudobonds, 570 residues, 13 models selected
Fab 3C11 Light Chain [ID: 1] region 6 chains [1-97] + 2 other blocks RMSD:
25.676
> select #4/L:2-102 #6/L:2-102 #17/L:2-102 #24/L:2-102 #33/L:2-102 #39/L:2-102
4308 atoms, 4422 bonds, 261 pseudobonds, 570 residues, 13 models selected
Fab 3C11 Light Chain [ID: 1] region 6 chains [1-97] + 3 other blocks RMSD:
25.676
> select clear
> select #4/L:80-84,122-128,184-188 #6/L:80-84,122-128,184-188
> #17/L:80-84,122-128,184-188 #24/L:80-84,122-128,184-188
> #33/L:80-84,122-128,184-188 #39/L:80-84,122-128,184-188
834 atoms, 828 bonds, 39 pseudobonds, 102 residues, 7 models selected
> select
> #4/L:5-6,11-14,20-26,33-39,46-52,63-68,71-76,85-91,98-99,103-107,115-119,130-140,146-151,154-156,160-164,174-183,192-198,206-211
> #6/L:5-6,11-14,20-26,33-39,46-52,63-68,71-76,85-91,98-99,103-107,115-119,130-140,146-151,154-156,160-164,174-183,192-198,206-211
> #17/L:5-6,11-14,20-26,33-39,46-52,63-68,71-76,85-91,98-99,103-107,115-119,130-140,146-151,154-156,160-164,174-183,192-198,206-211
> #24/L:5-6,11-14,20-26,33-39,46-52,63-68,71-76,85-91,98-99,103-107,115-119,130-140,146-151,154-156,160-164,174-183,192-198,206-211
> #33/L:5-6,11-14,20-26,33-39,46-52,63-68,71-76,85-91,98-99,103-107,115-119,130-140,146-151,154-156,160-164,174-183,192-198,206-211
> #39/L:5-6,11-14,20-26,33-39,46-52,63-68,71-76,85-91,98-99,103-107,115-119,130-140,146-151,154-156,160-164,174-183,192-198,206-211
4968 atoms, 4998 bonds, 292 pseudobonds, 636 residues, 7 models selected
> select clear
> select #4/L:2-102 #6/L:2-102 #17/L:2-102 #24/L:2-102 #33/L:2-102 #39/L:2-102
4308 atoms, 4422 bonds, 261 pseudobonds, 570 residues, 13 models selected
Fab 3C11 Light Chain [ID: 1] region 6 chains [1-102] RMSD: 25.676
> select #4/L:2-107 #6/L:2-107 #17/L:2-107 #24/L:2-107 #33/L:2-107 #39/L:2-107
4530 atoms, 4644 bonds, 286 pseudobonds, 600 residues, 13 models selected
Fab 3C11 Light Chain [ID: 1] region 6 chains [1-102] + 1 other block RMSD:
26.293
> open /Users/amy/Downloads/J1122_fit2.cif
Summary of feedback from opening /Users/amy/Downloads/J1122_fit2.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for J1122_fit2.cif #49
---
Chain | Description
Aa | No description available
Ab | No description available
Ac | No description available
Ad | No description available
Ae | No description available
Ba | No description available
Bb | No description available
Bc | No description available
Ca | No description available
Cb | No description available
Cc | No description available
> open /Users/amy/Downloads/J1122_fit2_raw.cif
Summary of feedback from opening /Users/amy/Downloads/J1122_fit2_raw.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for J1122_fit2_raw.cif #50
---
Chain | Description
0 5 BM CZ Co Cp Cy D4 DK DL DT DY DZ Dd Dk Do Dq EA U y | No description available
1 | No description available
2 A7 | No description available
3 t | No description available
4 x | No description available
6 | No description available
7 BF C5 Cj Cl Cn Cq D9 DP DQ Da Dm | No description available
8 | No description available
9 D8 | No description available
A | No description available
A0 | No description available
A1 | No description available
A2 | No description available
A3 AR Al | No description available
A4 | No description available
A5 | No description available
A6 | No description available
A8 r | No description available
A9 | No description available
AA | No description available
AB C7 | No description available
AC u | No description available
AD | No description available
AE An BA | No description available
AF | No description available
AG | No description available
AH | No description available
AI | No description available
AJ | No description available
AK DO | No description available
AL | No description available
AM | No description available
AN | No description available
AO | No description available
AP DD | No description available
AQ | No description available
AS | No description available
AT | No description available
AU | No description available
AV | No description available
AW | No description available
AX | No description available
AY | No description available
AZ | No description available
Aa | No description available
Ab | No description available
Ac | No description available
Ad | No description available
Ae | No description available
Af | No description available
Ag | No description available
Ah | No description available
Ai | No description available
Aj Ch Cw | No description available
Ak | No description available
Am | No description available
Ao | No description available
Ap | No description available
Aq | No description available
Ar | No description available
As | No description available
At | No description available
Au DS | No description available
Av | No description available
Aw Ck | No description available
Ax Ci | No description available
Ay | No description available
Az | No description available
B | No description available
B0 | No description available
B1 | No description available
B2 | No description available
B3 | No description available
B4 | No description available
B5 | No description available
B6 | No description available
B7 | No description available
B8 | No description available
B9 | No description available
BB | No description available
BC | No description available
BD | No description available
BE | No description available
BG | No description available
BH | No description available
BI | No description available
BJ | No description available
BK | No description available
BL | No description available
BN | No description available
BO | No description available
BP | No description available
BQ | No description available
BR | No description available
BS | No description available
BT | No description available
BU | No description available
BV | No description available
BW | No description available
BX | No description available
BY | No description available
BZ | No description available
Ba | No description available
Bb | No description available
Bc | No description available
Bd | No description available
Be | No description available
Bf | No description available
Bg | No description available
Bh | No description available
Bi | No description available
Bj | No description available
Bk | No description available
Bl | No description available
Bm | No description available
Bn | No description available
Bo DA DE DR Dh Dw Dz | No description available
Bp | No description available
Bq | No description available
Br | No description available
Bs | No description available
Bt | No description available
Bu | No description available
Bv | No description available
Bw | No description available
Bx | No description available
By | No description available
Bz | No description available
C | No description available
C0 C1 C2 Cr Ct Cv Cx DF DU DW Dl Dr Ds Dx s | No description available
C3 | No description available
C4 D3 | No description available
C6 D0 D5 | No description available
C8 | No description available
C9 DX | No description available
CA | No description available
CB | No description available
CC | No description available
CD | No description available
CE | No description available
CF | No description available
CG | No description available
CH | No description available
CI | No description available
CJ | No description available
CK | No description available
CL | No description available
CM | No description available
CN | No description available
CO | No description available
CP | No description available
CQ | No description available
CR | No description available
CS | No description available
CT | No description available
CU | No description available
CV | No description available
CW | No description available
CX | No description available
CY | No description available
Ca Cc D7 DV l | No description available
Cb | No description available
Cd Di Dt | No description available
Ce Df | No description available
Cf DJ Du | No description available
Cg | No description available
Cm | No description available
Cs Dc | No description available
Cu | No description available
Cz DI | No description available
D | No description available
D1 DH | No description available
D2 DB | No description available
D6 | No description available
DC Z | No description available
DG | No description available
DM | No description available
DN | No description available
Db | No description available
De | No description available
Dg | No description available
Dj | No description available
Dn | No description available
Dp | No description available
Dv | No description available
Dy | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
V | No description available
W p | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
m | No description available
n | No description available
o | No description available
q | No description available
v | No description available
w | No description available
z | No description available
> hide sel & #!39 atoms
> show sel & #!39 cartoons
> hide sel & #!39 surfaces
> hide sel & #!39 atoms
> hide sel & #!39 cartoons
> show sel & #!39 cartoons
> select add #33
6965 atoms, 7140 bonds, 287 pseudobonds, 922 residues, 14 models selected
> select subtract #33
3775 atoms, 3870 bonds, 274 pseudobonds, 500 residues, 11 models selected
> select clear
> hide #50#!39,49 atoms
> show #50#!39,49 cartoons
Computing secondary structure
> hide #!39 models
> hide #50 models
> show #50 models
> hide #!49 models
> show #50 atoms
> style #50 stick
Changed 9637 atom styles
> hide #50 cartoons
> hbonds #50 reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 8pi2 #35/A ARG 101 NE
12126 hydrogen bonds found
> select #29
2 models selected
> select #29
2 models selected
> select clear
> select #50/H: 23
10 atoms, 10 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #50/CR: 3
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel byhetero
> distance #50/H:23@O 50£/CR:3@ND2
Expected a keyword
> distance #50/H:23@O #50/CR:3@ND2
Distance between J1122_fit2_raw.cif #50/H HIS 23 O and /CR ASN 3 ND2: 2.742Å
> show #!39 models
> hide #50 models
> show #!39 atoms
> hide #!39 cartoons
> show #50 models
> hide #50 models
> show #50 models
> ui tool show "Show Sequence Viewer"
> sequence chain #4/L #6/L #17/L #24/L #33/L #39/L
Alignment identifier is 2
> hide #50 models
> show #50 models
> hide #50 models
> select
> #4/L:5-6,11-14,20-26,33-39,46-52,63-68,71-76,85-91,98-99,103-107,115-119,130-140,146-151,154-156,160-164,174-183,192-198,206-211
> #6/L:5-6,11-14,20-26,33-39,46-52,63-68,71-76,85-91,98-99,103-107,115-119,130-140,146-151,154-156,160-164,174-183,192-198,206-211
> #17/L:5-6,11-14,20-26,33-39,46-52,63-68,71-76,85-91,98-99,103-107,115-119,130-140,146-151,154-156,160-164,174-183,192-198,206-211
> #24/L:5-6,11-14,20-26,33-39,46-52,63-68,71-76,85-91,98-99,103-107,115-119,130-140,146-151,154-156,160-164,174-183,192-198,206-211
> #33/L:5-6,11-14,20-26,33-39,46-52,63-68,71-76,85-91,98-99,103-107,115-119,130-140,146-151,154-156,160-164,174-183,192-198,206-211
> #39/L:5-6,11-14,20-26,33-39,46-52,63-68,71-76,85-91,98-99,103-107,115-119,130-140,146-151,154-156,160-164,174-183,192-198,206-211
4968 atoms, 4998 bonds, 636 residues, 6 models selected
> select clear
> select #4/L:32-33 #6/L:32-33 #17/L:32-33 #24/L:32-33 #33/L:32-33 #39/L:32-33
96 atoms, 90 bonds, 12 residues, 6 models selected
> select #4/L:32-33 #6/L:32-33 #17/L:32-33 #24/L:32-33 #33/L:32-33 #39/L:32-33
96 atoms, 90 bonds, 12 residues, 6 models selected
Fab 3C11 Light Chain [ID: 2] region 6 chains [32-33] RMSD: 11.231
> show #50 models
> select clear
> select #4/L #6/L #17/L #24/L #33/L #39/L
9480 atoms, 9714 bonds, 6 pseudobonds, 1248 residues, 12 models selected
Fab 3C11 Light Chain [ID: 2] region 6 chains [1-215] RMSD: 54.353
> save /Users/amy/Desktop/lightchain format fasta alignment 2
> select clear
> hide #!39 models
> hide #50 models
> show #!49 models
> hide #!49 cartoons
> show #!49 atoms
> hide #!49 cartoons
> style #!49 stick
Changed 1939 atom styles
> hbonds #!49 reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 8pi2 #35/A ARG 101 NE
3318 hydrogen bonds found
> sequence chain
> #1/A#5/A#16/A#19/A#23/A#26/A#31/A#32/A#37/A#42/C#43/C#44/C#39/A
Alignment identifier is 3
> sequence chain
> #1/B#5/B#16/B#19/B#23/B#26/B#31/B#32/B#37/B#42/B#43/B#44/B#39/C
Alignment identifier is 4
> sequence chain #4/H#6/H#17/H#24/H#33/H#39/H
Alignment identifier is 5
> sequence chain #4/L#6/L#17/L#24/L#33/L#39/L
Alignment identifier is 6
> sequence chain #7/A#18/A#20/A#25/A#42/A#43/A#44/A
Alignment identifier is 7
> sequence chain #19/C#26/C#32/C#30/B#37/C#57/C
Alignment identifier is 8
> sequence chain #27/B#36/B#39/B
Alignment identifier is 9
> sequence chain #35/A
Alignment identifier is 35/A
> sequence chain #36/A
Alignment identifier is 36/A
> sequence chain #38/A
Alignment identifier is 38/A
> sequence chain #38/B
Alignment identifier is 38/B
> sequence chain #38/H
Alignment identifier is 38/H
> sequence chain #38/L
Alignment identifier is 38/L
> sequence chain #40/Ba
Alignment identifier is 40/Ba
> sequence chain #40/Ca
Alignment identifier is 40/Ca
> sequence chain #40/Aa
Alignment identifier is 40/Aa
> sequence chain #40/Bb
Alignment identifier is 40/Bb
> sequence chain #40/Ab
Alignment identifier is 40/Ab
> sequence chain #40/Cb
Alignment identifier is 40/Cb
> sequence chain #40/Cc
Alignment identifier is 40/Cc
> sequence chain #40/Cd
Alignment identifier is 40/Cd
> sequence chain #46/A
Alignment identifier is 46/A
> sequence chain #46/B
Alignment identifier is 46/B
> sequence chain #46/C
Alignment identifier is 46/C
> sequence chain #46/D
Alignment identifier is 46/D
> sequence chain #46/E
Alignment identifier is 46/E
> sequence chain #46/F
Alignment identifier is 46/F
> sequence chain #46/G
Alignment identifier is 46/G
> sequence chain #46/H
Alignment identifier is 46/H
> sequence chain #46/I
Alignment identifier is 46/I
> sequence chain #46/J
Alignment identifier is 46/J
> sequence chain #46/K
Alignment identifier is 46/K
> sequence chain #46/L
Alignment identifier is 46/L
> sequence chain #46/M
Alignment identifier is 46/M
> sequence chain #46/N
Alignment identifier is 46/N
> sequence chain #46/O
Alignment identifier is 46/O
> sequence chain #46/P
Alignment identifier is 46/P
> sequence chain #46/Q
Alignment identifier is 46/Q
> sequence chain #46/R#50/j
Alignment identifier is 10
> sequence chain #46/S,p,Bw,B3,C1,DW,Dj,Dy#50/Bo,DA,DE,DR,Dh,Dw,Dz
Alignment identifier is 11
> sequence chain #46/T#50/Ag
Alignment identifier is 12
> sequence chain #46/U
Alignment identifier is 46/U
> sequence chain #46/V,X,3
Alignment identifier is 13
> sequence chain #46/W,Dz,D2#50/Ay
Alignment identifier is 14
> sequence chain #46/Y
Alignment identifier is 46/Y
> sequence chain #46/Z
Alignment identifier is 46/Z
> sequence chain #46/a
Alignment identifier is 46/a
> sequence chain #46/b,l,Av#50/a
Alignment identifier is 15
> sequence chain #46/c
Alignment identifier is 46/c
> sequence chain #46/d
Alignment identifier is 46/d
> sequence chain #46/e,Bq#50/u,AC
Alignment identifier is 16
> sequence chain #46/f
Alignment identifier is 46/f
> sequence chain #46/g,r,Az
Alignment identifier is 17
> sequence chain
> #46/h,o,Ay,BQ,Bl,Bm,CW,Ce,Cg,Cp,Cs,Cu,C8,DC,DH,DL,DN,Dg,Dh,Dk,Dq,Dt,D3,D5#50/U,y,0,5,BM,CZ,Co,Cp,Cy,DK,DL,DT,DY,DZ,Dd,Dk,Do,Dq,D4,EA
Alignment identifier is 18
> sequence chain #46/i,y
Alignment identifier is 19
> sequence chain
> #46/j,CZ,Cz,DF,Da,De,Df,D6#50/7,BF,Cj,Cl,Cn,Cq,C5,DP,DQ,Da,Dm,D9
Alignment identifier is 20
> sequence chain #46/k,Ca
Alignment identifier is 21
> sequence chain #46/m
Alignment identifier is 46/m
> sequence chain #46/n
Alignment identifier is 46/n
> sequence chain
> #46/q,AH,An,Cl,C0,C2,C9,DE,DS,Dv,Dw#50/s,Cr,Ct,Cv,Cx,C0,C1,C2,DF,DU,DW,Dl,Dr,Ds,Dx
Alignment identifier is 22
> sequence chain #46/s
Alignment identifier is 46/s
> sequence chain #46/t
Alignment identifier is 46/t
> sequence chain #46/u
Alignment identifier is 46/u
> sequence chain #46/v
Alignment identifier is 46/v
> sequence chain #46/w
Alignment identifier is 46/w
> sequence chain #46/x
Alignment identifier is 46/x
> sequence chain #46/z,AF#50/6
Alignment identifier is 23
> sequence chain #46/0
Alignment identifier is 46/0
> sequence chain #46/1
Alignment identifier is 46/1
> sequence chain #46/2
Alignment identifier is 46/2
> sequence chain #46/4
Alignment identifier is 46/4
> sequence chain #46/5
Alignment identifier is 46/5
> sequence chain #46/6
Alignment identifier is 46/6
> sequence chain #46/7
Alignment identifier is 46/7
> sequence chain #46/8
Alignment identifier is 46/8
> sequence chain #46/9
Alignment identifier is 46/9
> sequence chain #46/AA
Alignment identifier is 46/AA
> sequence chain #46/AB
Alignment identifier is 46/AB
> sequence chain #46/AC
Alignment identifier is 46/AC
> sequence chain #46/AD
Alignment identifier is 46/AD
> sequence chain #46/AE#50/AZ
Alignment identifier is 24
> sequence chain #46/AG
Alignment identifier is 46/AG
> sequence chain #46/AI,CY#50/Cf,DJ,Du
Alignment identifier is 25
> sequence chain #46/AJ
Alignment identifier is 46/AJ
> sequence chain #46/AK
Alignment identifier is 46/AK
> sequence chain #46/AL
Alignment identifier is 46/AL
> sequence chain #46/AM
Alignment identifier is 46/AM
> sequence chain #46/AN
Alignment identifier is 46/AN
> sequence chain #46/AO
Alignment identifier is 46/AO
> sequence chain #46/AP
Alignment identifier is 46/AP
> sequence chain #46/AQ
Alignment identifier is 46/AQ
> sequence chain #46/AR
Alignment identifier is 46/AR
> sequence chain #46/AS
Alignment identifier is 46/AS
> sequence chain #46/AT
Alignment identifier is 46/AT
> sequence chain #46/AU
Alignment identifier is 46/AU
> sequence chain #46/AV
Alignment identifier is 46/AV
> sequence chain #46/AW
Alignment identifier is 46/AW
> sequence chain #46/AX
Alignment identifier is 46/AX
> sequence chain #46/AY
Alignment identifier is 46/AY
> sequence chain #46/AZ
Alignment identifier is 46/AZ
> sequence chain #46/Aa
Alignment identifier is 46/Aa
> sequence chain #46/Ab
Alignment identifier is 46/Ab
> sequence chain #46/Ac
Alignment identifier is 46/Ac
> sequence chain #46/Ad
Alignment identifier is 46/Ad
> sequence chain #46/Ae
Alignment identifier is 46/Ae
> sequence chain #46/Af
Alignment identifier is 46/Af
> sequence chain #46/Ag
Alignment identifier is 46/Ag
> sequence chain #46/Ah
Alignment identifier is 46/Ah
> sequence chain #46/Ai
Alignment identifier is 46/Ai
> sequence chain #46/Aj
Alignment identifier is 46/Aj
> sequence chain #46/Ak
Alignment identifier is 46/Ak
> sequence chain #46/Al,Cr,Cx,DP#50/Cm
Alignment identifier is 26
> sequence chain #46/Am#50/C4,D3
Alignment identifier is 27
> sequence chain #46/Ao
Alignment identifier is 46/Ao
> sequence chain #46/Ap
Alignment identifier is 46/Ap
> sequence chain #46/Aq
Alignment identifier is 46/Aq
> sequence chain #46/Ar
Alignment identifier is 46/Ar
> sequence chain #46/As
Alignment identifier is 46/As
> sequence chain #46/At
Alignment identifier is 46/At
> sequence chain #46/Au
Alignment identifier is 46/Au
> sequence chain #46/Aw
Alignment identifier is 46/Aw
> sequence chain #46/Ax
Alignment identifier is 46/Ax
> sequence chain #46/A0
Alignment identifier is 46/A0
> sequence chain #46/A1
Alignment identifier is 46/A1
> sequence chain #46/A2#50/AR,Al,A3
Alignment identifier is 28
> sequence chain #46/A3
Alignment identifier is 46/A3
> sequence chain #46/A4#50/A1
Alignment identifier is 29
> sequence chain #46/A5
Alignment identifier is 46/A5
> sequence chain #46/A6#50/v
Alignment identifier is 30
> sequence chain #46/A7
Alignment identifier is 46/A7
> sequence chain #46/A8
Alignment identifier is 46/A8
> sequence chain #46/A9
Alignment identifier is 46/A9
> sequence chain #46/BA
Alignment identifier is 46/BA
> sequence chain #46/BB
Alignment identifier is 46/BB
> sequence chain #46/BC
Alignment identifier is 46/BC
> sequence chain #46/BD
Alignment identifier is 46/BD
> sequence chain #46/BE
Alignment identifier is 46/BE
> sequence chain #46/BF
Alignment identifier is 46/BF
> sequence chain #46/BG
Alignment identifier is 46/BG
> sequence chain #46/BH
Alignment identifier is 46/BH
> sequence chain #46/BI
Alignment identifier is 46/BI
> sequence chain #46/BJ
Alignment identifier is 46/BJ
> sequence chain #46/BK
Alignment identifier is 46/BK
> sequence chain #46/BL
Alignment identifier is 46/BL
> sequence chain #46/BM
Alignment identifier is 46/BM
> sequence chain #46/BN
Alignment identifier is 46/BN
> sequence chain #46/BO
Alignment identifier is 46/BO
> sequence chain #46/BP
Alignment identifier is 46/BP
> sequence chain #46/BR
Alignment identifier is 46/BR
> sequence chain #46/BS
Alignment identifier is 46/BS
> sequence chain #46/BT,Dp,D4#50/DH,D1
Alignment identifier is 31
> sequence chain #46/BU
Alignment identifier is 46/BU
> sequence chain #46/BV
Alignment identifier is 46/BV
> sequence chain #46/BW
Alignment identifier is 46/BW
> sequence chain #46/BX
Alignment identifier is 46/BX
> sequence chain #46/BY
Alignment identifier is 46/BY
> sequence chain #46/BZ
Alignment identifier is 46/BZ
> sequence chain #46/Ba
Alignment identifier is 46/Ba
> sequence chain #46/Bb
Alignment identifier is 46/Bb
> sequence chain #46/Bc
Alignment identifier is 46/Bc
> sequence chain #46/Bd
Alignment identifier is 46/Bd
> sequence chain #46/Be
Alignment identifier is 46/Be
> sequence chain #46/Bf
Alignment identifier is 46/Bf
> sequence chain #46/Bg
Alignment identifier is 46/Bg
> sequence chain #46/Bh
Alignment identifier is 46/Bh
> sequence chain #46/Bi
Alignment identifier is 46/Bi
> sequence chain #46/Bj
Alignment identifier is 46/Bj
> sequence chain #46/Bk
Alignment identifier is 46/Bk
> sequence chain #46/Bn
Alignment identifier is 46/Bn
> sequence chain #46/Bo
Alignment identifier is 46/Bo
> sequence chain #46/Bp
Alignment identifier is 46/Bp
> sequence chain #46/Br
Alignment identifier is 46/Br
> sequence chain #46/Bs
Alignment identifier is 46/Bs
> sequence chain #46/Bt
Alignment identifier is 46/Bt
> sequence chain #46/Bu
Alignment identifier is 46/Bu
> sequence chain #46/Bv
Alignment identifier is 46/Bv
> sequence chain #46/Bx
Alignment identifier is 46/Bx
> sequence chain #46/By
Alignment identifier is 46/By
> sequence chain #46/Bz
Alignment identifier is 46/Bz
> sequence chain #46/B0,Ck#50/C3
Alignment identifier is 32
> sequence chain #46/B1
Alignment identifier is 46/B1
> sequence chain #46/B2
Alignment identifier is 46/B2
> sequence chain #46/B4
Alignment identifier is 46/B4
> sequence chain #46/B5
Alignment identifier is 46/B5
> sequence chain #46/B6
Alignment identifier is 46/B6
> sequence chain #46/B7
Alignment identifier is 46/B7
> sequence chain #46/B8
Alignment identifier is 46/B8
> sequence chain #46/B9
Alignment identifier is 46/B9
> sequence chain #46/CA
Alignment identifier is 46/CA
> sequence chain #46/CB
Alignment identifier is 46/CB
> sequence chain #46/CC
Alignment identifier is 46/CC
> sequence chain #46/CD
Alignment identifier is 46/CD
> sequence chain #46/CE
Alignment identifier is 46/CE
> sequence chain #46/CF
Alignment identifier is 46/CF
> sequence chain #46/CG
Alignment identifier is 46/CG
> sequence chain #46/CH
Alignment identifier is 46/CH
> sequence chain #46/CI
Alignment identifier is 46/CI
> sequence chain #46/CJ
Alignment identifier is 46/CJ
> sequence chain #46/CK
Alignment identifier is 46/CK
> sequence chain #46/CL
Alignment identifier is 46/CL
> sequence chain #46/CM
Alignment identifier is 46/CM
> sequence chain #46/CN
Alignment identifier is 46/CN
> sequence chain #46/CO
Alignment identifier is 46/CO
> sequence chain #46/CP
Alignment identifier is 46/CP
> sequence chain #46/CQ
Alignment identifier is 46/CQ
> sequence chain #46/CR
Alignment identifier is 46/CR
> sequence chain #46/CS
Alignment identifier is 46/CS
> sequence chain #46/CT
Alignment identifier is 46/CT
> sequence chain #46/CU
Alignment identifier is 46/CU
> sequence chain #46/CV#50/DM
Alignment identifier is 33
> sequence chain #46/CX
Alignment identifier is 46/CX
> sequence chain #46/Cb,DA,Ds#50/Cs,Dc
Alignment identifier is 34
> sequence chain #46/Cc
Alignment identifier is 46/Cc
> sequence chain #46/Cd
Alignment identifier is 46/Cd
> sequence chain #46/Cf,Dm
Alignment identifier is 35
> sequence chain #46/Ch
Alignment identifier is 46/Ch
> sequence chain #46/Ci,DQ#50/Ce,Df
Alignment identifier is 36
> sequence chain #46/Cj#50/Db
Alignment identifier is 37
> sequence chain #46/Cm#50/l,Ca,Cc,DV,D7
Alignment identifier is 38
> sequence chain #46/Cn#50/Ax,Ci
Alignment identifier is 39
> sequence chain #46/Co,DB,Dd
Alignment identifier is 40
> sequence chain #46/Cq,Dr#50/t,3
Alignment identifier is 41
> sequence chain #46/Ct,DM#50/Dv
Alignment identifier is 42
> sequence chain #46/Cv,C6,D0#50/Cu
Alignment identifier is 43
> sequence chain #46/Cw
Alignment identifier is 46/Cw
> sequence chain #46/Cy
Alignment identifier is 46/Cy
> sequence chain #46/C3
Alignment identifier is 46/C3
> sequence chain #46/C4
Alignment identifier is 46/C4
> sequence chain #46/C5#50/AB,C7
Alignment identifier is 44
> sequence chain #46/C7
Alignment identifier is 46/C7
> sequence chain #46/DD
Alignment identifier is 46/DD
> sequence chain #46/DG#50/Aj,Ch,Cw
Alignment identifier is 45
> sequence chain #46/DI
Alignment identifier is 46/DI
> sequence chain #46/DJ
Alignment identifier is 46/DJ
> sequence chain #46/DK
Alignment identifier is 46/DK
> sequence chain #46/DO#50/Cd,Di,Dt
Alignment identifier is 46
> sequence chain #46/DR
Alignment identifier is 46/DR
> sequence chain #46/DT#50/Ap
Alignment identifier is 47
> sequence chain #46/DU
Alignment identifier is 46/DU
> sequence chain #46/DV#50/W,p
Alignment identifier is 48
> sequence chain #46/DX,Db#50/DN
Alignment identifier is 49
> sequence chain #46/DY#50/9,D8
Alignment identifier is 50
> sequence chain #46/DZ#50/C9,DX
Alignment identifier is 51
> sequence chain #46/Dc#50/n
Alignment identifier is 52
> sequence chain #46/Di,Dl,Do#50/AI
Alignment identifier is 53
> sequence chain #46/Dn
Alignment identifier is 46/Dn
> sequence chain #46/Du
Alignment identifier is 46/Du
> sequence chain #46/Dx
Alignment identifier is 46/Dx
> sequence chain #46/D1
Alignment identifier is 46/D1
> sequence chain #46/D7
Alignment identifier is 46/D7
> sequence chain #49/Aa
Alignment identifier is 49/Aa
> sequence chain #49/Ab
Alignment identifier is 49/Ab
> sequence chain #49/Ca
Alignment identifier is 49/Ca
> sequence chain #49/Ba
Alignment identifier is 49/Ba
> sequence chain #49/Bb
Alignment identifier is 49/Bb
> sequence chain #49/Ac
Alignment identifier is 49/Ac
> sequence chain #49/Cb
Alignment identifier is 49/Cb
> sequence chain #49/Cc
Alignment identifier is 49/Cc
> sequence chain #49/Bc
Alignment identifier is 49/Bc
> sequence chain #49/Ad
Alignment identifier is 49/Ad
> sequence chain #49/Ae
Alignment identifier is 49/Ae
> sequence chain #50/A
Alignment identifier is 50/A
> sequence chain #50/B
Alignment identifier is 50/B
> sequence chain #50/C
Alignment identifier is 50/C
> sequence chain #50/D
Alignment identifier is 50/D
> sequence chain #50/E
Alignment identifier is 50/E
> sequence chain #50/F
Alignment identifier is 50/F
> sequence chain #50/G
Alignment identifier is 50/G
> sequence chain #50/H
Alignment identifier is 50/H
> sequence chain #50/I
Alignment identifier is 50/I
> sequence chain #50/J
Alignment identifier is 50/J
> sequence chain #50/K
Alignment identifier is 50/K
> sequence chain #50/L
Alignment identifier is 50/L
> sequence chain #50/M
Alignment identifier is 50/M
> sequence chain #50/N
Alignment identifier is 50/N
> sequence chain #50/O
Alignment identifier is 50/O
> sequence chain #50/P
Alignment identifier is 50/P
> sequence chain #50/Q
Alignment identifier is 50/Q
> sequence chain #50/R
Alignment identifier is 50/R
> sequence chain #50/S
Alignment identifier is 50/S
> sequence chain #50/T
Alignment identifier is 50/T
> sequence chain #50/V
Alignment identifier is 50/V
> sequence chain #50/X
Alignment identifier is 50/X
> sequence chain #50/Y
Alignment identifier is 50/Y
> sequence chain #50/Z,DC
Alignment identifier is 54
> sequence chain #50/b
Alignment identifier is 50/b
> sequence chain #50/c
Alignment identifier is 50/c
> sequence chain #50/d
Alignment identifier is 50/d
> sequence chain #50/e
Alignment identifier is 50/e
> sequence chain #50/f
Alignment identifier is 50/f
> sequence chain #50/g
Alignment identifier is 50/g
> sequence chain #50/h
Alignment identifier is 50/h
> sequence chain #50/i
Alignment identifier is 50/i
> sequence chain #50/k
Alignment identifier is 50/k
> sequence chain #50/m
Alignment identifier is 50/m
> sequence chain #50/o
Alignment identifier is 50/o
> sequence chain #50/q
Alignment identifier is 50/q
> sequence chain #50/r,A8
Alignment identifier is 55
> sequence chain #50/w
Alignment identifier is 50/w
> sequence chain #50/x,4
Alignment identifier is 56
> sequence chain #50/z
Alignment identifier is 50/z
> sequence chain #50/1
Alignment identifier is 50/1
> sequence chain #50/2,A7
Alignment identifier is 57
> sequence chain #50/8
Alignment identifier is 50/8
> sequence chain #50/AA
Alignment identifier is 50/AA
> sequence chain #50/AD
Alignment identifier is 50/AD
> sequence chain #50/AE,An,BA
Alignment identifier is 58
> sequence chain #50/AF
Alignment identifier is 50/AF
> sequence chain #50/AG
Alignment identifier is 50/AG
> sequence chain #50/AH
Alignment identifier is 50/AH
> sequence chain #50/AJ
Alignment identifier is 50/AJ
> sequence chain #50/AK,DO
Alignment identifier is 59
> sequence chain #50/AL
Alignment identifier is 50/AL
> sequence chain #50/AM
Alignment identifier is 50/AM
> sequence chain #50/AN
Alignment identifier is 50/AN
> sequence chain #50/AO
Alignment identifier is 50/AO
> sequence chain #50/AP,DD
Alignment identifier is 60
> sequence chain #50/AQ
Alignment identifier is 50/AQ
> sequence chain #50/AS
Alignment identifier is 50/AS
> sequence chain #50/AT
Alignment identifier is 50/AT
> sequence chain #50/AU
Alignment identifier is 50/AU
> sequence chain #50/AV
Alignment identifier is 50/AV
> sequence chain #50/AW
Alignment identifier is 50/AW
> sequence chain #50/AX
Alignment identifier is 50/AX
> sequence chain #50/AY
Alignment identifier is 50/AY
> sequence chain #50/Aa
Alignment identifier is 50/Aa
> sequence chain #50/Ab
Alignment identifier is 50/Ab
> sequence chain #50/Ac
Alignment identifier is 50/Ac
> sequence chain #50/Ad
Alignment identifier is 50/Ad
> sequence chain #50/Ae
Alignment identifier is 50/Ae
> sequence chain #50/Af
Alignment identifier is 50/Af
> sequence chain #50/Ah
Alignment identifier is 50/Ah
> sequence chain #50/Ai
Alignment identifier is 50/Ai
> sequence chain #50/Ak
Alignment identifier is 50/Ak
> sequence chain #50/Am
Alignment identifier is 50/Am
> sequence chain #50/Ao
Alignment identifier is 50/Ao
> sequence chain #50/Aq
Alignment identifier is 50/Aq
> sequence chain #50/Ar
Alignment identifier is 50/Ar
> sequence chain #50/As
Alignment identifier is 50/As
> sequence chain #50/At
Alignment identifier is 50/At
> sequence chain #50/Au,DS
Alignment identifier is 61
> sequence chain #50/Av
Alignment identifier is 50/Av
> sequence chain #50/Aw,Ck
Alignment identifier is 62
> sequence chain #50/Az
Alignment identifier is 50/Az
> sequence chain #50/A0
Alignment identifier is 50/A0
> sequence chain #50/A2
Alignment identifier is 50/A2
> sequence chain #50/A4
Alignment identifier is 50/A4
> sequence chain #50/A5
Alignment identifier is 50/A5
> sequence chain #50/A6
Alignment identifier is 50/A6
> sequence chain #50/A9
Alignment identifier is 50/A9
> sequence chain #50/BB
Alignment identifier is 50/BB
> sequence chain #50/BC
Alignment identifier is 50/BC
> sequence chain #50/BD
Alignment identifier is 50/BD
> sequence chain #50/BE
Alignment identifier is 50/BE
> sequence chain #50/BG
Alignment identifier is 50/BG
> sequence chain #50/BH
Alignment identifier is 50/BH
> sequence chain #50/BI
Alignment identifier is 50/BI
> sequence chain #50/BJ
Alignment identifier is 50/BJ
> sequence chain #50/BK
Alignment identifier is 50/BK
> sequence chain #50/BL
Alignment identifier is 50/BL
> sequence chain #50/BN
Alignment identifier is 50/BN
> sequence chain #50/BO
Alignment identifier is 50/BO
> sequence chain #50/BP
Alignment identifier is 50/BP
> sequence chain #50/BQ
Alignment identifier is 50/BQ
> sequence chain #50/BR
Alignment identifier is 50/BR
> sequence chain #50/BS
Alignment identifier is 50/BS
> sequence chain #50/BT
Alignment identifier is 50/BT
> sequence chain #50/BU
Alignment identifier is 50/BU
> sequence chain #50/BV
Alignment identifier is 50/BV
> sequence chain #50/BW
Alignment identifier is 50/BW
> sequence chain #50/BX
Alignment identifier is 50/BX
> sequence chain #50/BY
Alignment identifier is 50/BY
> sequence chain #50/BZ
Alignment identifier is 50/BZ
> sequence chain #50/Ba
Alignment identifier is 50/Ba
> sequence chain #50/Bb
Alignment identifier is 50/Bb
> sequence chain #50/Bc
Alignment identifier is 50/Bc
> sequence chain #50/Bd
Alignment identifier is 50/Bd
> sequence chain #50/Be
Alignment identifier is 50/Be
> sequence chain #50/Bf
Alignment identifier is 50/Bf
> sequence chain #50/Bg
Alignment identifier is 50/Bg
> sequence chain #50/Bh
Alignment identifier is 50/Bh
> sequence chain #50/Bi
Alignment identifier is 50/Bi
> sequence chain #50/Bj
Alignment identifier is 50/Bj
> sequence chain #50/Bk
Alignment identifier is 50/Bk
> sequence chain #50/Bl
Alignment identifier is 50/Bl
> sequence chain #50/Bm
Alignment identifier is 50/Bm
> sequence chain #50/Bn
Alignment identifier is 50/Bn
> sequence chain #50/Bp
Alignment identifier is 50/Bp
> sequence chain #50/Bq
Alignment identifier is 50/Bq
> sequence chain #50/Br
Alignment identifier is 50/Br
> sequence chain #50/Bs
Alignment identifier is 50/Bs
> sequence chain #50/Bt
Alignment identifier is 50/Bt
> sequence chain #50/Bu
Alignment identifier is 50/Bu
> sequence chain #50/Bv
Alignment identifier is 50/Bv
> sequence chain #50/Bw
Alignment identifier is 50/Bw
> sequence chain #50/Bx
Alignment identifier is 50/Bx
> sequence chain #50/By
Alignment identifier is 50/By
> sequence chain #50/Bz
Alignment identifier is 50/Bz
> sequence chain #50/B0
Alignment identifier is 50/B0
> sequence chain #50/B1
Alignment identifier is 50/B1
> sequence chain #50/B2
Alignment identifier is 50/B2
> sequence chain #50/B3
Alignment identifier is 50/B3
> sequence chain #50/B4
Alignment identifier is 50/B4
> sequence chain #50/B5
Alignment identifier is 50/B5
> sequence chain #50/B6
Alignment identifier is 50/B6
> sequence chain #50/B7
Alignment identifier is 50/B7
> sequence chain #50/B8
Alignment identifier is 50/B8
> sequence chain #50/B9
Alignment identifier is 50/B9
> sequence chain #50/CA
Alignment identifier is 50/CA
> sequence chain #50/CB
Alignment identifier is 50/CB
> sequence chain #50/CC
Alignment identifier is 50/CC
> sequence chain #50/CD
Alignment identifier is 50/CD
> sequence chain #50/CE
Alignment identifier is 50/CE
> sequence chain #50/CF
Alignment identifier is 50/CF
> sequence chain #50/CG
Alignment identifier is 50/CG
> sequence chain #50/CH
Alignment identifier is 50/CH
> sequence chain #50/CI
Alignment identifier is 50/CI
> sequence chain #50/CJ
Alignment identifier is 50/CJ
> sequence chain #50/CK
Alignment identifier is 50/CK
> sequence chain #50/CL
Alignment identifier is 50/CL
> sequence chain #50/CM
Alignment identifier is 50/CM
> sequence chain #50/CN
Alignment identifier is 50/CN
> sequence chain #50/CO
Alignment identifier is 50/CO
> sequence chain #50/CP
Alignment identifier is 50/CP
> sequence chain #50/CQ
Alignment identifier is 50/CQ
> sequence chain #50/CR
Alignment identifier is 50/CR
> sequence chain #50/CS
Alignment identifier is 50/CS
> sequence chain #50/CT
Alignment identifier is 50/CT
> sequence chain #50/CU
Alignment identifier is 50/CU
> sequence chain #50/CV
Alignment identifier is 50/CV
> sequence chain #50/CW
Alignment identifier is 50/CW
> sequence chain #50/CX
Alignment identifier is 50/CX
> sequence chain #50/CY
Alignment identifier is 50/CY
> sequence chain #50/Cb
Alignment identifier is 50/Cb
> sequence chain #50/Cg
Alignment identifier is 50/Cg
> sequence chain #50/Cz,DI
Alignment identifier is 63
> sequence chain #50/C6,D0,D5
Alignment identifier is 64
> sequence chain #50/C8
Alignment identifier is 50/C8
> sequence chain #50/DB,D2
Alignment identifier is 65
> sequence chain #50/DG
Alignment identifier is 50/DG
> sequence chain #50/De
Alignment identifier is 50/De
> sequence chain #50/Dg
Alignment identifier is 50/Dg
> sequence chain #50/Dj
Alignment identifier is 50/Dj
> sequence chain #50/Dn
Alignment identifier is 50/Dn
> sequence chain #50/Dp
Alignment identifier is 50/Dp
> sequence chain #50/Dy
Alignment identifier is 50/Dy
> sequence chain #50/D6
Alignment identifier is 50/D6
===== Log before crash end =====
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M5
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: Mac17,2
Model Number: MDE64B/A
Chip: Apple M5
Total Number of Cores: 10 (4 Super and 6 Efficiency)
Memory: 24 GB
System Firmware Version: 13822.81.10
OS Loader Version: 13822.81.10
Software:
System Software Overview:
System Version: macOS 26.3.1 (a) (25D771280a)
Kernel Version: Darwin 25.3.0
Time since boot: 8天23分钟
Graphics/Displays:
Apple M5:
Chipset Model: Apple M5
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 XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL P2314H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.1
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-ArtiaX: 0.6.0
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
geomdl: 5.4.0
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
pandas: 3.0.1
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
pyarrow: 23.0.1
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
starfile: 0.5.13
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
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
AFAIK, there is a confirmation dialog for any of the ways of opening a large number of sequence viewers, so either the user requested this or I missed some path to opening a large number of viewers. Either way, there's nothing I can do about it without contact info.