The following bug report has been submitted:
Platform: macOS-15.5-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Current thread 0x0000000206a35f00 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, 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.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.spatial._ckdtree, scipy._lib.messagestream, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, markupsafe._speedups, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, openmm._openmm, openmm.app.internal.compiled, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.alignment_algs._sw, chimerax.alignment_algs._nw (total: 98)
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/gzl289/Downloads/cryosparc_P42_J567_map_EM-Ready2.mrc
Opened cryosparc_P42_J567_map_EM-Ready2.mrc as #1, grid size 466,466,466,
pixel 0.5, shown at level 2.08, step 2, values float32
> volume #1 level 2.837
> volume #1 step 1
> volume #1 level 5.805
> open /Users/gzl289/Downloads/output_no_seq_RTE.cif
Summary of feedback from opening /Users/gzl289/Downloads/output_no_seq_RTE.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for output_no_seq_RTE.cif #2
---
Chain | Description
1 | No description available
2 Ak C6 FY | No description available
3 | No description available
5 | No description available
6 | No description available
7 | No description available
8 G8 | No description available
9 Al CG E1 GF | No description available
A | No description available
A0 | No description available
A4 | No description available
A6 It | No description available
A8 | No description available
A9 AT Ah Aq Bu Cf Cw Cy DV Ds E5 EJ EQ Eu F1 FK Fo GN HO f l | No description available
AB Dt | No description available
AC | No description available
AE JP | No description available
AI Br V | No description available
AK | No description available
AL Bd | No description available
AM G2 | No description available
AN | No description available
AP | No description available
AQ | No description available
AR Aj Dz E7 FI Gu | No description available
AS | No description available
AV | No description available
AX | No description available
AY | No description available
Ad | No description available
Ae B4 Bo Bz | No description available
Af | No description available
Ag | No description available
Am | No description available
An G3 | No description available
Ao | No description available
As Bp CS D6 DO EL Ee Hu | No description available
Av | No description available
Ax | No description available
Az | No description available
B | No description available
B2 Dr | No description available
B5 CA | No description available
B6 BF | No description available
B7 | No description available
B9 | No description available
BA Jh | No description available
BC | No description available
BD Cm DJ FC | No description available
BE | No description available
BJ EE M | No description available
BK Bk CM Dm | No description available
BM BW Cq | No description available
BN | No description available
BO | No description available
BQ | No description available
BR IB | No description available
BS | No description available
BT | No description available
BY FB FW w | No description available
Bg | No description available
Bi Dj | No description available
Bj N | No description available
Bm | No description available
Bn | No description available
Bq | No description available
Bs | No description available
C | No description available
C2 Dw | No description available
C7 DR | No description available
CD | No description available
CE CV CX D2 m | No description available
CP | No description available
CQ | No description available
CT j | No description available
CU | No description available
CW | No description available
Ce | No description available
Ch | No description available
Ci | No description available
Cn | No description available
Co | No description available
Cp | No description available
Cr | No description available
Cz DS | No description available
D | No description available
D7 | No description available
D9 | No description available
DA | No description available
DB | No description available
DC | No description available
DG GM | No description available
DT | No description available
DY | No description available
Dc Et | No description available
Dd | No description available
Dp FH Gc | No description available
Dq | No description available
Dy | No description available
E | No description available
E4 | No description available
E6 | No description available
E8 | No description available
E9 a | No description available
EC | No description available
EN | No description available
ER | No description available
EV | No description available
Ek Fl Fs K | No description available
Ep S | No description available
Eq | No description available
Ev | No description available
Ey u | No description available
Ez Hr Jw | No description available
F | No description available
F5 | No description available
FA | No description available
FD | No description available
FG | No description available
FL | No description available
FO | No description available
FR | No description available
FS | No description available
FT | No description available
FZ G4 | No description available
Fh | No description available
Fi | No description available
Fm | No description available
Fn | No description available
Fp | No description available
Fw | No description available
Fz | No description available
G | No description available
G9 | No description available
GA | No description available
GC | No description available
GE | No description available
GH | No description available
Gd | No description available
Gn | No description available
Go v | No description available
Gr | No description available
Gz | No description available
H | No description available
H0 | No description available
H1 | No description available
H2 | No description available
H3 | No description available
H4 | No description available
H5 | No description available
H6 | No description available
H7 | No description available
H8 | No description available
H9 | No description available
HB | No description available
HD | No description available
HG HL | No description available
HH | No description available
HK | No description available
HM | No description available
HP | No description available
HQ | No description available
HR | No description available
HS | No description available
HT | No description available
HU | No description available
HV | No description available
HW | No description available
HX | No description available
HY | No description available
HZ | No description available
Ha | No description available
Hb | No description available
Hc | No description available
Hd | No description available
He | No description available
Hf | No description available
Hg | No description available
Hh | No description available
Hi | No description available
Hj | No description available
Hk | No description available
Hl | No description available
Hm | No description available
Hn | No description available
Ho | No description available
Hp | No description available
Hq | No description available
Hs | No description available
Ht | No description available
Hv | No description available
Hw | No description available
Hx | No description available
Hy | No description available
Hz | No description available
I0 | No description available
I1 | No description available
I2 | No description available
I3 | No description available
I4 | No description available
I5 | No description available
I6 | No description available
I7 | No description available
I8 | No description available
I9 | No description available
IA | No description available
IC | No description available
ID | No description available
IE | No description available
IF | No description available
IG | No description available
IH | No description available
II | No description available
IJ | No description available
IK | No description available
IL | No description available
IM | No description available
IN | No description available
IO | No description available
IP | No description available
IQ | No description available
IR | No description available
IS | No description available
IT | No description available
IU | No description available
IV | No description available
IW | No description available
IX | No description available
IY | No description available
IZ | No description available
Ia | No description available
Ib | No description available
Ic | No description available
Id | No description available
Ie | No description available
If | No description available
Ig | No description available
Ih | No description available
Ii | No description available
Ij | No description available
Ik | No description available
Il | No description available
Im | No description available
In | No description available
Io | No description available
Ip | No description available
Iq | No description available
Ir | No description available
Is | No description available
Iu | No description available
Iv | No description available
Iw | No description available
Ix | No description available
Iy | No description available
Iz | No description available
J | No description available
J0 | No description available
J1 | No description available
J2 | No description available
J3 | No description available
J4 | No description available
J5 | No description available
J6 | No description available
J7 | No description available
J8 | No description available
J9 | No description available
JA | No description available
JB | No description available
JC | No description available
JD | No description available
JE | No description available
JF | No description available
JG | No description available
JH | No description available
JI | No description available
JJ | No description available
JK | No description available
JL | No description available
JM | No description available
JN | No description available
JO | No description available
JQ | No description available
JR | No description available
JS | No description available
JT | No description available
JU | No description available
JV | No description available
JW | No description available
JX | No description available
JY | No description available
JZ | No description available
Ja | No description available
Jb | No description available
Jc | No description available
Jd | No description available
Je | No description available
Jf | No description available
Jg | No description available
Ji | No description available
Jj | No description available
Jk | No description available
Jl | No description available
Jm | No description available
Jn | No description available
Jo | No description available
Jp | No description available
Jq | No description available
Jr | No description available
Js | No description available
Jt | No description available
Ju | No description available
Jv | No description available
Jx | No description available
Jy | No description available
Jz | No description available
KA | No description available
KB | No description available
KC | No description available
KD | No description available
KE | No description available
KF | No description available
KG | No description available
KH | No description available
KI | No description available
KJ | No description available
KK | No description available
KL | No description available
KM | No description available
KN | No description available
KO | No description available
KP | No description available
KQ | No description available
KR | No description available
KS | No description available
KT | No description available
KU | No description available
KV | No description available
KW | No description available
KX | No description available
KY | No description available
KZ | No description available
Ka | No description available
Kb | No description available
Kc | No description available
Kd | No description available
Ke | No description available
Kf | No description available
Kg | No description available
Kh | No description available
Ki | No description available
Kj | No description available
Kk | No description available
Kl | No description available
Km | No description available
Kn | No description available
Ko | No description available
Kp | No description available
Kq | No description available
Kr | No description available
Ks | No description available
Kt | No description available
Ku | No description available
Kv | No description available
Kw | No description available
Kx | No description available
Ky | No description available
L | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
T | No description available
U | No description available
W | No description available
X | No description available
Z | No description available
b | No description available
g | No description available
i | No description available
k | No description available
n | No description available
o | No description available
p | No description available
r | No description available
x | No description available
> hide atoms
> show cartoons
> select /Ja:1739-1742
21 atoms, 20 bonds, 4 residues, 1 model selected
> select /Ja:1739-1742
21 atoms, 20 bonds, 4 residues, 1 model selected
> select /Ja:1739-1742
21 atoms, 20 bonds, 4 residues, 1 model selected
> select /3:139-141
17 atoms, 16 bonds, 3 residues, 1 model selected
> select /3:139-141
17 atoms, 16 bonds, 3 residues, 1 model selected
> select /3:139-141
17 atoms, 16 bonds, 3 residues, 1 model selected
> transparency 50
> set bgColor white
Alignment identifier is 2/3
> select add #2
15146 atoms, 14685 bonds, 2233 residues, 1 model selected
Alignment identifier is 2/A
Alignment identifier is 2/B
Alignment identifier is 2/C
Alignment identifier is 2/D
Alignment identifier is 2/E
Alignment identifier is 2/F
Alignment identifier is 2/G
Alignment identifier is 2/H
Alignment identifier is 2/J
Alignment identifier is 1
Alignment identifier is 2/L
Alignment identifier is 2
Alignment identifier is 3
Alignment identifier is 2/O
Alignment identifier is 2/P
Alignment identifier is 2/Q
Alignment identifier is 2/R
Alignment identifier is 4
Alignment identifier is 2/T
Alignment identifier is 2/U
Alignment identifier is 5
Alignment identifier is 2/W
Alignment identifier is 2/X
Alignment identifier is 2/Z
Alignment identifier is 6
Alignment identifier is 2/b
Alignment identifier is 7
Alignment identifier is 2/g
Alignment identifier is 2/i
Alignment identifier is 8
Alignment identifier is 2/k
Alignment identifier is 9
Alignment identifier is 2/n
Alignment identifier is 2/o
Alignment identifier is 2/p
Alignment identifier is 2/r
Alignment identifier is 10
Alignment identifier is 11
Alignment identifier is 12
Alignment identifier is 2/x
Alignment identifier is 2/1
Alignment identifier is 13
Alignment identifier is 2/3
Alignment identifier is 2/5
Alignment identifier is 2/6
Alignment identifier is 2/7
Alignment identifier is 14
Alignment identifier is 15
Alignment identifier is 16
Alignment identifier is 2/AC
Alignment identifier is 17
Alignment identifier is 2/AK
Alignment identifier is 18
Alignment identifier is 19
Alignment identifier is 2/AN
Alignment identifier is 2/AP
Alignment identifier is 2/AQ
Alignment identifier is 20
Alignment identifier is 2/AS
Alignment identifier is 2/AV
Alignment identifier is 2/AX
Alignment identifier is 2/AY
Alignment identifier is 2/Ad
Alignment identifier is 21
Alignment identifier is 2/Af
Alignment identifier is 2/Ag
Alignment identifier is 2/Am
Alignment identifier is 22
Alignment identifier is 2/Ao
Alignment identifier is 23
Alignment identifier is 2/Av
Alignment identifier is 2/Ax
Alignment identifier is 2/Az
Alignment identifier is 2/A0
Alignment identifier is 2/A4
Alignment identifier is 24
Alignment identifier is 2/A8
Alignment identifier is 25
Alignment identifier is 2/BC
Alignment identifier is 26
Alignment identifier is 2/BE
Alignment identifier is 27
Alignment identifier is 28
Alignment identifier is 29
Alignment identifier is 2/BN
Alignment identifier is 2/BO
Alignment identifier is 2/BQ
Alignment identifier is 30
Alignment identifier is 2/BS
Alignment identifier is 2/BT
Alignment identifier is 2/Bg
Alignment identifier is 31
Alignment identifier is 2/Bm
Alignment identifier is 2/Bn
Alignment identifier is 2/Bq
Alignment identifier is 2/Bs
Alignment identifier is 32
Alignment identifier is 33
Alignment identifier is 2/B7
Alignment identifier is 2/B9
Alignment identifier is 2/CD
Alignment identifier is 2/CP
Alignment identifier is 2/CQ
Alignment identifier is 2/CU
Alignment identifier is 2/CW
Alignment identifier is 2/Ce
Alignment identifier is 2/Ch
Alignment identifier is 2/Ci
Alignment identifier is 2/Cn
Alignment identifier is 2/Co
Alignment identifier is 2/Cp
Alignment identifier is 2/Cr
Alignment identifier is 34
Alignment identifier is 35
Alignment identifier is 36
Alignment identifier is 2/DA
Alignment identifier is 2/DB
Alignment identifier is 2/DC
Alignment identifier is 37
Alignment identifier is 2/DT
Alignment identifier is 2/DY
Alignment identifier is 38
Alignment identifier is 2/Dd
Alignment identifier is 39
Alignment identifier is 2/Dq
Alignment identifier is 2/Dy
Alignment identifier is 2/D7
Alignment identifier is 2/D9
Alignment identifier is 2/EC
Alignment identifier is 2/EN
Alignment identifier is 2/ER
Alignment identifier is 2/EV
Alignment identifier is 2/Eq
Alignment identifier is 2/Ev
Alignment identifier is 40
Alignment identifier is 2/E4
Alignment identifier is 2/E6
Alignment identifier is 2/E8
Alignment identifier is 2/FA
Alignment identifier is 2/FD
Alignment identifier is 2/FG
Alignment identifier is 2/FL
Alignment identifier is 2/FO
Alignment identifier is 2/FR
Alignment identifier is 2/FS
Alignment identifier is 2/FT
Alignment identifier is 41
Alignment identifier is 2/Fh
Alignment identifier is 2/Fi
Alignment identifier is 2/Fm
Alignment identifier is 2/Fn
Alignment identifier is 2/Fp
Alignment identifier is 2/Fw
Alignment identifier is 2/Fz
Alignment identifier is 2/F5
Alignment identifier is 2/GA
Alignment identifier is 2/GC
Alignment identifier is 2/GE
Alignment identifier is 2/GH
Alignment identifier is 2/Gd
Alignment identifier is 2/Gn
Alignment identifier is 2/Gr
Alignment identifier is 2/Gz
Alignment identifier is 2/G9
Alignment identifier is 2/HB
Alignment identifier is 2/HD
Alignment identifier is 42
Alignment identifier is 2/HH
Alignment identifier is 2/HK
Alignment identifier is 2/HM
Alignment identifier is 2/HP
Alignment identifier is 2/HQ
Alignment identifier is 2/HR
Alignment identifier is 2/HS
Alignment identifier is 2/HT
Alignment identifier is 2/HU
Alignment identifier is 2/HV
Alignment identifier is 2/HW
Alignment identifier is 2/HX
Alignment identifier is 2/HY
Alignment identifier is 2/HZ
Alignment identifier is 2/Ha
Alignment identifier is 2/Hb
Alignment identifier is 2/Hc
Alignment identifier is 2/Hd
Alignment identifier is 2/He
Alignment identifier is 2/Hf
Alignment identifier is 2/Hg
Alignment identifier is 2/Hh
Alignment identifier is 2/Hi
Alignment identifier is 2/Hj
Alignment identifier is 2/Hk
Alignment identifier is 2/Hl
Alignment identifier is 2/Hm
Alignment identifier is 2/Hn
Alignment identifier is 2/Ho
Alignment identifier is 2/Hp
Alignment identifier is 2/Hq
Alignment identifier is 2/Hs
Alignment identifier is 2/Ht
Alignment identifier is 2/Hv
Alignment identifier is 2/Hw
Alignment identifier is 2/Hx
Alignment identifier is 2/Hy
Alignment identifier is 2/Hz
Alignment identifier is 2/H0
Alignment identifier is 2/H1
Alignment identifier is 2/H2
Alignment identifier is 2/H3
Alignment identifier is 2/H4
Alignment identifier is 2/H5
Alignment identifier is 2/H6
Alignment identifier is 2/H7
Alignment identifier is 2/H8
Alignment identifier is 2/H9
Alignment identifier is 2/IA
Alignment identifier is 2/IC
Alignment identifier is 2/ID
Alignment identifier is 2/IE
Alignment identifier is 2/IF
Alignment identifier is 2/IG
Alignment identifier is 2/IH
Alignment identifier is 2/II
Alignment identifier is 2/IJ
Alignment identifier is 2/IK
Alignment identifier is 2/IL
Alignment identifier is 2/IM
Alignment identifier is 2/IN
Alignment identifier is 2/IO
Alignment identifier is 2/IP
Alignment identifier is 2/IQ
Alignment identifier is 2/IR
Alignment identifier is 2/IS
Alignment identifier is 2/IT
Alignment identifier is 2/IU
Alignment identifier is 2/IV
Alignment identifier is 2/IW
Alignment identifier is 2/IX
Alignment identifier is 2/IY
Alignment identifier is 2/IZ
Alignment identifier is 2/Ia
Alignment identifier is 2/Ib
Alignment identifier is 2/Ic
Alignment identifier is 2/Id
Alignment identifier is 2/Ie
Alignment identifier is 2/If
Alignment identifier is 2/Ig
Alignment identifier is 2/Ih
Alignment identifier is 2/Ii
Alignment identifier is 2/Ij
Alignment identifier is 2/Ik
Alignment identifier is 2/Il
Alignment identifier is 2/Im
Alignment identifier is 2/In
Alignment identifier is 2/Io
Alignment identifier is 2/Ip
Alignment identifier is 2/Iq
Alignment identifier is 2/Ir
Alignment identifier is 2/Is
Alignment identifier is 2/Iu
Alignment identifier is 2/Iv
Alignment identifier is 2/Iw
Alignment identifier is 2/Ix
Alignment identifier is 2/Iy
Alignment identifier is 2/Iz
Alignment identifier is 2/I0
Alignment identifier is 2/I1
Alignment identifier is 2/I2
Alignment identifier is 2/I3
Alignment identifier is 2/I4
Alignment identifier is 2/I5
Alignment identifier is 2/I6
Alignment identifier is 2/I7
Alignment identifier is 2/I8
Alignment identifier is 2/I9
Alignment identifier is 2/JA
Alignment identifier is 2/JB
Alignment identifier is 2/JC
Alignment identifier is 2/JD
Alignment identifier is 2/JE
Alignment identifier is 2/JF
Alignment identifier is 2/JG
Alignment identifier is 2/JH
Alignment identifier is 2/JI
Alignment identifier is 2/JJ
Alignment identifier is 2/JK
Alignment identifier is 2/JL
Alignment identifier is 2/JM
Alignment identifier is 2/JN
Alignment identifier is 2/JO
Alignment identifier is 2/JQ
Alignment identifier is 2/JR
Alignment identifier is 2/JS
Alignment identifier is 2/JT
Alignment identifier is 2/JU
Alignment identifier is 2/JV
Alignment identifier is 2/JW
Alignment identifier is 2/JX
Alignment identifier is 2/JY
Alignment identifier is 2/JZ
Alignment identifier is 2/Ja
Alignment identifier is 2/Jb
Alignment identifier is 2/Jc
Alignment identifier is 2/Jd
Alignment identifier is 2/Je
Alignment identifier is 2/Jf
Alignment identifier is 2/Jg
Alignment identifier is 2/Ji
Alignment identifier is 2/Jj
Alignment identifier is 2/Jk
Alignment identifier is 2/Jl
Alignment identifier is 2/Jm
Alignment identifier is 2/Jn
Alignment identifier is 2/Jo
Alignment identifier is 2/Jp
Alignment identifier is 2/Jq
Alignment identifier is 2/Jr
Alignment identifier is 2/Js
Alignment identifier is 2/Jt
Alignment identifier is 2/Ju
Alignment identifier is 2/Jv
Alignment identifier is 2/Jx
Alignment identifier is 2/Jy
Alignment identifier is 2/Jz
Alignment identifier is 2/J0
Alignment identifier is 2/J1
Alignment identifier is 2/J2
Alignment identifier is 2/J3
Alignment identifier is 2/J4
Alignment identifier is 2/J5
Alignment identifier is 2/J6
Alignment identifier is 2/J7
Alignment identifier is 2/J8
Alignment identifier is 2/J9
Alignment identifier is 2/KA
Alignment identifier is 2/KB
Alignment identifier is 2/KC
Alignment identifier is 2/KD
Alignment identifier is 2/KE
Alignment identifier is 2/KF
Alignment identifier is 2/KG
Alignment identifier is 2/KH
Alignment identifier is 2/KI
Alignment identifier is 2/KJ
Alignment identifier is 2/KK
Alignment identifier is 2/KL
Alignment identifier is 2/KM
Alignment identifier is 2/KN
Alignment identifier is 2/KO
Alignment identifier is 2/KP
Alignment identifier is 2/KQ
Alignment identifier is 2/KR
Alignment identifier is 2/KS
Alignment identifier is 2/KT
Alignment identifier is 2/KU
Alignment identifier is 2/KV
Alignment identifier is 2/KW
Alignment identifier is 2/KX
Alignment identifier is 2/KY
Alignment identifier is 2/KZ
Alignment identifier is 2/Ka
Alignment identifier is 2/Kb
Alignment identifier is 2/Kc
Alignment identifier is 2/Kd
Alignment identifier is 2/Ke
Alignment identifier is 2/Kf
Alignment identifier is 2/Kg
Alignment identifier is 2/Kh
Alignment identifier is 2/Ki
Alignment identifier is 2/Kj
Alignment identifier is 2/Kk
Alignment identifier is 2/Kl
Alignment identifier is 2/Km
Alignment identifier is 2/Kn
Alignment identifier is 2/Ko
Alignment identifier is 2/Kp
Alignment identifier is 2/Kq
Alignment identifier is 2/Kr
Alignment identifier is 2/Ks
Alignment identifier is 2/Kt
Alignment identifier is 2/Ku
Alignment identifier is 2/Kv
Alignment identifier is 2/Kw
Alignment identifier is 2/Kx
Alignment identifier is 2/Ky
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/MCM_DH_MA_maternal.cif
Summary of feedback from opening
/Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/MCM_DH_MA_maternal.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for MCM_DH_MA_maternal.cif #1
---
Chain | Description
Aa | No description available
Ab | No description available
Ac | No description available
Ba | No description available
Bb | No description available
Bc | No description available
Bd | No description available
Be | No description available
Ca | No description available
Cb | No description available
Cc | No description available
Cd | No description available
Da | No description available
Db | No description available
Dc | No description available
Dd | No description available
De | No description available
Ea | No description available
Eb | No description available
Ec | No description available
Ed Ee | No description available
Ef | No description available
Eg | No description available
Eh | No description available
Fa | No description available
Fb | No description available
Fc | No description available
> open
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/MCM_DH_MA_zygotic.cif
Summary of feedback from opening
/Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/MCM_DH_MA_zygotic.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for MCM_DH_MA_zygotic.cif #2
---
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
Bd | No description available
Be | No description available
Bf | No description available
Ca | No description available
Cb | No description available
Cc | No description available
Cd | No description available
Ce | No description available
Da | No description available
Db | No description available
Dc | No description available
Ea | No description available
Eb | No description available
Fa | No description available
Fb | No description available
Fc | No description available
Fd | No description available
Fe | No description available
Ff | No description available
Fg | No description available
Ga | No description available
Ha | No description available
Hb | No description available
Hc Hg | No description available
Hd | No description available
He | No description available
Hf | No description available
Hh | No description available
Hi | No description available
Ia | No description available
Ib | No description available
> open
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/MCM_DH_MA_no_seq.cif
Summary of feedback from opening
/Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/MCM_DH_MA_no_seq.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for MCM_DH_MA_no_seq.cif #3
---
Chain | Description
2 | No description available
4 | No description available
9 | No description available
A | No description available
A0 | No description available
A1 | No description available
A2 | No description available
A3 | No description available
A4 | No description available
A5 | No description available
A6 | No description available
A7 | No description available
A8 | No description available
A9 | No description available
AA | No description available
AC | No description available
AD | No description available
AG | No description available
AW | No description available
AX | No description available
AY | No description available
Ak | 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
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
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 | 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 | 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
CA | No description available
CB | No description available
CC | No description available
CD | No description available
CE | No description available
D | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
O | No description available
R | No description available
T | No description available
V | No description available
W | No description available
X | No description available
a | No description available
b | No description available
d | No description available
f | No description available
j | No description available
k | No description available
m | No description available
n | No description available
q | No description available
r | No description available
t | No description available
u | No description available
v | No description available
z | No description available
> hide #!1 models
> hide #!2 models
> hide #3 models
> show #3 models
> hide #3 atoms
> show #3 cartoons
> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/MCM_DH_NO_SEQ_MA.pdb
> models #3
> open
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/Xenopus_nucleosome/NCP/NCP_No_Seq.cif
Summary of feedback from opening
/Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/Xenopus_nucleosome/NCP/NCP_No_Seq.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for NCP_No_Seq.cif #4
---
Chain | Description
A | No description available
C | No description available
J | 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
> hide #3 models
> hide #4 atoms
> show #4 cartoons
> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/Xenopus_nucleosome/NCP/NCP_no_seq.pdb
> models #4
> hide #4 models
> show #!1 models
> hide #!1 atoms
> show #!1 cartoons
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,6
Model Number: MRX33DK/A
Chip: Apple M3 Pro
Total Number of Cores: 11 (5 performance and 6 efficiency)
Memory: 18 GB
System Firmware Version: 11881.121.1
OS Loader Version: 11881.121.1
Software:
System Software Overview:
System Version: macOS 15.5 (24F74)
Kernel Version: Darwin 24.5.0
Time since boot: 6 days, 23 hours, 17 minutes
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Support: Metal 3
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
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
biopython: 1.83
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.23.1
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.8
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
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
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.3.7
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
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
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
DiffFit: 0.6.2
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
fsspec: 2024.10.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
mpmath: 1.3.0
mrcfile: 1.5.0
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
Send2Trash: 1.8.3
SEQCROW: 1.8.16
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
sympy: 1.13.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
torch: 2.2.1
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Unusual to see a graphics crash with a Mac ARM GPU. The user had a large atomic model open (~100 chains).