Crash saving PNG

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1160.59.1.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00007f73067fc700 (most recent call first):
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 316 in wait
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 574 in wait
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 1284 in run
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Current thread 0x00007f737d305740 (most recent call first):
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PIL/ImageFile.py", line 518 in _save
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PIL/PngImagePlugin.py", line 1349 in _save
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PIL/Image.py", line 2235 in save
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/image_formats/save.py", line 123 in save_image
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/image_formats/__init__.py", line 45 in save
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/save_command/cmd.py", line 89 in provider_save
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2856 in run
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/save_command/cmd.py", line 75 in cmd_save
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2856 in run
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 36 in run
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py", line 512 in run
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py", line 1254 in save_image
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py", line 327 in run
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py", line 408 in run_shortcut
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py", line 390 in try_shortcut
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py", line 1334 in run_provider
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/shortcuts/__init__.py", line 52 in run_provider
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/toolshed/__init__.py", line 1284 in run_provider
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/toolshed/info.py", line 381 in run_provider
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/toolbar/tool.py", line 165 in callback
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in 
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 87 in _run_code
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /mnt/enki-data/zqiao/mitoribosome-zl/7-yMRC1_resampled-emready.mrc
> format mrc

Opened 7-yMRC1_resampled-emready.mrc as #1, grid size 441,441,441, pixel 1,
shown at level 3.4, step 2, values float32  

> open /mnt/enki-data/zqiao/mitoribosome-zl/D_MRC1_Oct30.cif

Summary of feedback from opening /mnt/enki-data/zqiao/mitoribosome-
zl/D_MRC1_Oct30.cif  
---  
warnings | Unknown polymer entity '1' near line 374  
Unknown polymer entity '2' near line 699  
Unknown polymer entity '3' near line 3574  
Unknown polymer entity '4' near line 4518  
Unknown polymer entity '5' near line 5565  
70 messages similar to the above omitted  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for D_MRC1_Oct30.cif #2  
---  
Chain | Description  
0 | ?  
1 | ?  
2 | ?  
3 | ?  
4 | ?  
5 | ?  
6 | ?  
7 | ?  
8 | ?  
9 | ?  
A | ?  
AA | ?  
AB | ?  
AC | ?  
AD | ?  
AE | ?  
AF | ?  
AG | ?  
AH | ?  
AI | ?  
AJ | ?  
AK | ?  
AL | ?  
AM | ?  
B | ?  
C | ?  
D | ?  
E | ?  
F | ?  
G | ?  
H | ?  
I | ?  
J | ?  
K | ?  
L | ?  
M | ?  
N | ?  
O | ?  
P | ?  
Q | ?  
R | ?  
S | ?  
T | ?  
U | ?  
V | ?  
W | ?  
X | ?  
Y | ?  
Z | ?  
a | ?  
b | ?  
c | ?  
d | ?  
e | ?  
f | ?  
g | ?  
h | ?  
i | ?  
j | ?  
k | ?  
l | ?  
m | ?  
n | ?  
o | ?  
p | ?  
q | ?  
r | ?  
s | ?  
t | ?  
u | ?  
v | ?  
w | ?  
x | ?  
y | ?  
z | ?  
  

> open /mnt/enki-data/zqiao/mitoribosome-zl/5mrc.cif

Summary of feedback from opening /mnt/enki-data/zqiao/mitoribosome-zl/5mrc.cif  
---  
warnings | Unknown polymer entity '82' near line 233829  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
5mrc.cif title:  
Structure of the yeast mitochondrial ribosome - Class A [more info...]  
  
Chain information for 5mrc.cif #3  
---  
Chain | Description | UniProt  
0 | bL36m | RTC6_YEAST  
1 | mL38 | RM35_YEAST  
11 | mS38 | COX24_YEAST  
2 | mL40 | RM28_YEAST  
22 | mS41 | FYV4_YEAST  
3 | mL41 | RM27_YEAST  
33 | mS42 | RT26_YEAST  
4 | mL43 | RM51_YEAST  
44 | mS43 | RT01_YEAST  
5 | mL44 | RM03_YEAST  
55 | mS44 | RT13_YEAST  
6 | mL46 | RM17_YEAST  
66 | mS45 | RT35_YEAST  
7 | mL49 | IMG2_YEAST  
77 | mS46 | RSM28_YEAST  
8 | mL50 | RM13_YEAST  
88 | mS47 | HIBCH_YEAST  
9 | mL57 | RM15_YEAST  
A | 21S ribosomal RNA |  
AA | bS1m | RT51_YEAST  
B | uL2m | RML2_YEAST  
BB | uS2m | RT04_YEAST  
C | uL3m | RM09_YEAST  
CC | uS3m | RMAR_YEAST  
D | uL4m | RL4P_YEAST  
DD | uS4m | NAM9_YEAST  
E | uL5m | RM07_YEAST  
EE | uS5m | RT05_YEAST  
F | uL6m | RM06_YEAST  
FF | bS6m | RT06_YEAST  
G | bL9m | RM50_YEAST  
GG | uS7m | RT07_YEAST  
H | uL13m | RM23_YEAST  
HH | uS8m | RT08_YEAST  
I | uL14m | RM38_YEAST  
II | uS9m | RT09_YEAST  
J | uL15m | RM10_YEAST  
JJ | uS10m | RT10_YEAST  
K | uL16m | RM16_YEAST  
KK | uS11m | RT18_YEAST  
L | bL17m | RM08_YEAST  
LL | uS12m | RT12_YEAST  
M | bL19m | IMG1_YEAST  
MM | uS13m | SWS2_YEAST  
N | bL21m | RN49_YEAST  
NN | uS14m | RT02_YEAST  
O | uL22m | RM22_YEAST  
OO | uS15m | RT28_YEAST  
P | uL23m | RM41_YEAST  
PP | bS16m | RT16_YEAST  
Q | uL24m | RM40_YEAST  
QQ | uS17m | RT17_YEAST  
R | bL27m | RM02_YEAST  
RR | bS18m | RSM18_YEAST  
S | bL28m | RM24_YEAST  
SS | uS19m | RT19_YEAST  
T | uL29m | RM04_YEAST  
TT | bS21m | RT21_YEAST  
U | uL30m | RM33_YEAST  
UU | mS23 | RT25_YEAST  
V | bL31m | RM36_YEAST  
VV | mS26 | RTPT_YEAST  
W | bL32m | RM32_YEAST  
WW | mS29 | RT23_YEAST  
X | bL33m | RM39_YEAST  
XX | mS33 | RT27_YEAST  
Y | bL34m | RM34_YEAST  
YY | mS35 | RT24_YEAST  
Z | bL35m | YNM2_YEAST  
ZZ | mS37 | MRP10_YEAST  
a | mL58 | RM20_YEAST  
aa | 15S ribosomal RNA |  
b | mL59 | RM25_YEAST  
bb | tRNA |  
c | mL60 | RM31_YEAST  
cc | unknown protein sequence 1 |  
d | mL67 | MHR1_YEAST  
dd | unknown protein sequence 2 |  
  
Non-standard residues in 5mrc.cif #3  
---  
MG — magnesium ion  
NA — sodium ion  
ZN — zinc ion  
  

> hide atoms

> hide cartoons

> set bgColor white

> lighting soft

> show /A,AM cartoons

> hide #!1 models

> color #3 cyan

> color #2 lime

> color #2 tan

> color #3 #303030

> color #3 #808080

> color #2/AM salmon

> save /home/zqiao/Desktop/image2.png supersample 3


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 545.23.08
OpenGL renderer: NVIDIA GeForce GTX 1080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Supermicro
Model: SYS-7048GR-TR
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 40 Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz
Cache Size: 25600 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           125G        5.9G        8.0G        177M        111G        118G
	Swap:           31G        1.9G         30G

Graphics:
	02:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [GeForce GTX 1080 Ti] [10de:1b06] (rev a1)	
	Subsystem: eVga.com. Corp. Device [3842:5390]	
	Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.3
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0