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#5411 closed defect (can't reproduce)

Hung saving TIFF?

Reported by:	chimerax-bug-report@…	Owned by:	Tom Goddard
Priority:	normal	Milestone:
Component:	Input/Output	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Linux-4.4.0-210-generic-x86_64-with-glibc2.14
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /scratch2/jrai/hpc_mountoint/jrai/21may22d/Refine3D/job050/run_ct13_class001.mrc

Opened run_ct13_class001.mrc as #1, grid size 256,256,256, pixel 1.07, shown
at level 0.00917, step 1, values float32  

> set bgColor white

> volume #1 level 0.006097

> volume #1 level 0.003599

> open /disks/li/d1/Jay/19sep13a/Finalstructures/run_ct14_class001.mrc

Opened run_ct14_class001.mrc as #2, grid size 256,256,256, pixel 1.07, shown
at level 0.0149, step 1, values float32  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 8010, resource id:
11625610, major code: 40 (TranslateCoords), minor code: 0  

> close #1

> volume #2 level 0.01076

> graphics silhouettes true width 5 depthJump 0.2 colorblack

Expected a keyword  

> graphics silhouettes true width 5 depthJump 0.2 color black

> transparency #2 100

> graphics silhouettes true width 5 depthJump 0.3 color black

> graphics silhouettes true width 5 depthJump 0.5 color black

> graphics silhouettes true width 5 depthJump 0.1 color black

> graphics silhouettes true width 5 depthJump 0.05 color black

> open
> /scratch2/jrai/mountpoint12tb/21may/P19/J148/cryosparc_P19_J148_class_00_00122_volume.mrc
> /scratch2/jrai/mountpoint12tb/21may/P19/J148/cryosparc_P19_J148_class_01_00122_volume.mrc
> /scratch2/jrai/mountpoint12tb/21may/P19/J148/cryosparc_P19_J148_class_02_00122_volume.mrc

Opened cryosparc_P19_J148_class_00_00122_volume.mrc as #1.1, grid size
128,128,128, pixel 2.15, shown at level 0.444, step 1, values float32  
Opened cryosparc_P19_J148_class_01_00122_volume.mrc as #1.2, grid size
128,128,128, pixel 2.15, shown at level 0.65, step 1, values float32  
Opened cryosparc_P19_J148_class_02_00122_volume.mrc as #1.3, grid size
128,128,128, pixel 2.15, shown at level 0.383, step 1, values float32  

> volume #2 level 0.006831

> volume #1.1 level 0.2766

> color #1 gray

> lighting soft

> lighting simple

> lighting full

> hide #!1.1 models

> hide #!1.2 models

> hide #!1.3 models

> show #!1.1 models

> lighting simple

> lighting soft

> lighting full

> lighting soft

> hide #!1.1 models

> show #!1.2 models

> hide #!1.2 models

> show #!1.3 models

> close #1.1

> close #1.2

> close #1.3

> open
> /scratch2/jrai/mountpoint12tb/21may/P19/J150/cryosparc_P19_J150_class_00_00122_volume.mrc

Opened cryosparc_P19_J150_class_00_00122_volume.mrc as #3, grid size
128,128,128, pixel 2.15, shown at level 0.615, step 1, values float32  

> color #3 gray

> open
> /scratch2/jrai/mountpoint12tb/21may/P19/J150/cryosparc_P19_J150_class_01_00122_volume.mrc

Opened cryosparc_P19_J150_class_01_00122_volume.mrc as #4, grid size
128,128,128, pixel 2.15, shown at level 0.681, step 1, values float32  

> open
> /scratch2/jrai/mountpoint12tb/21may/P19/J150/cryosparc_P19_J150_class_02_00122_volume.mrc

Opened cryosparc_P19_J150_class_02_00122_volume.mrc as #5, grid size
128,128,128, pixel 2.15, shown at level 0.653, step 1, values float32  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 51241, resource id:
11633465, major code: 40 (TranslateCoords), minor code: 0  

> volume #4 level 0.3291

> volume #3 level 0.4265

> volume #5 level 0.3788

> hide #!3 models

> hide #!4 models

> hide #!5 models

> show #!3 models

No map chosen to save  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 60790, resource id:
11634744, major code: 40 (TranslateCoords), minor code: 0  

> save /scratch2/jrai/mountpoint12tb/21may/Images/J150_class00.tiff

> show #!4 models

> hide #!3 models

> color #4 gray

> save /scratch2/jrai/mountpoint12tb/21may/Images/J150_class01.tiff

> hide #!4 models

> show #!5 models

> color #5 gray

> save /scratch2/jrai/mountpoint12tb/21may/Images/J150_class02.tiff

> close #3

> close #4

> close #5

> open
> /scratch2/jrai/hpc_mountoint/jrai/21may22d/PostProcess/job040/postprocess.mrc

Opened postprocess.mrc as #3, grid size 256,256,256, pixel 1.07, shown at
level 0.0103, step 1, values float32  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 6072, resource id:
11648632, major code: 40 (TranslateCoords), minor code: 0  

> fitmap #3 #2

Missing required "in_map" argument  

> fitmap #3 inMap #2

Fit map postprocess.mrc in map run_ct14_class001.mrc using 167668 points  
correlation = 0.9119, correlation about mean = 0.4922, overlap = 65.27  
steps = 236, shift = 12.1, angle = 20.6 degrees  
  
Position of postprocess.mrc (#3) relative to run_ct14_class001.mrc (#2)
coordinates:  
Matrix rotation and translation  
0.96813892 -0.17382027 -0.18025968 54.28506092  
0.12273318 0.95682775 -0.26347150 28.82644944  
0.21827415 0.23295317 0.94767569 -43.90133347  
Axis 0.70686609 -0.56747794 0.42226664  
Axis point 0.00000000 213.16701708 81.96713191  
Rotation angle (degrees) 20.55735072  
Shift along axis 3.47582605  
  

> surface dust #3

> volume #3 level 0.007796

> color #3 gray

> save /scratch2/jrai/mountpoint12tb/21may/Images/pp_job40.tiff

> hide #!3 models

> close #3

> open
> /scratch2/jrai/hpc_mountoint/jrai/21may22d/Class3D/job039/run_it025_class005.mrc
> /scratch2/jrai/hpc_mountoint/jrai/21may22d/Class3D/job039/run_it025_class004.mrc
> /scratch2/jrai/hpc_mountoint/jrai/21may22d/Class3D/job039/run_it025_class003.mrc
> /scratch2/jrai/hpc_mountoint/jrai/21may22d/Class3D/job039/run_it025_class002.mrc
> /scratch2/jrai/hpc_mountoint/jrai/21may22d/Class3D/job039/run_it025_class001.mrc

Opened run_it025_class005.mrc as #3.1, grid size 256,256,256, pixel 1.07,
shown at level 0.0119, step 1, values float32  
Opened run_it025_class004.mrc as #3.2, grid size 256,256,256, pixel 1.07,
shown at level 0.0102, step 1, values float32  
Opened run_it025_class003.mrc as #3.3, grid size 256,256,256, pixel 1.07,
shown at level 0.0111, step 1, values float32  
Opened run_it025_class002.mrc as #3.4, grid size 256,256,256, pixel 1.07,
shown at level 0.0127, step 1, values float32  
Opened run_it025_class001.mrc as #3.5, grid size 256,256,256, pixel 1.07,
shown at level 0.00887, step 1, values float32  

> fitmap #3 inMap #2

Multiple maps for #3  

> fitmap #3.1-3.5 inMap #2

No atoms or maps for #3.1-3.5  

> fitmap #2 inMap #3.1

Fit map run_ct14_class001.mrc in map run_it025_class005.mrc using 342747
points  
correlation = 0.8839, correlation about mean = 0.5114, overlap = 76.99  
steps = 212, shift = 11.4, angle = 20.4 degrees  
  
Position of run_ct14_class001.mrc (#2) relative to run_it025_class005.mrc
(#3.1) coordinates:  
Matrix rotation and translation  
0.96918677 0.11999885 0.21512153 -45.59826548  
-0.17061000 0.95694219 0.23484862 -8.41701514  
-0.17767730 -0.26431406 0.94792872 58.72385164  
Axis -0.71461679 0.56234302 -0.41604467  
Axis point 0.00000000 211.25372010 82.76188668  
Rotation angle (degrees) 20.44157025  
Shift along axis 3.42029095  
  

> hide #!3.1 models

> hide #!3.2 models

> hide #!3.3 models

> hide #!3.4 models

> hide #!3.5 models

> color #3 gray

> show #!3.1 models

> volume #3.1 level 0.005417

> hide #!3.1 models

> show #!3.2 models

> volume #3.2 level 0.005712

> hide #!3.2 models

> show #!3.3 models

> volume #3.2 level 0.003187

> hide #!3.2 models

> volume #3.3 level 0.005126

> volume #3.4 level 0.006421

> hide #!3.3 models

> hide #!3.4 models

> show #!3.5 models

> volume #3.5 level 0.004892

> hide #!3.5 models

> show #!3.4 models

> hide #!3.4 models

> show #!3.4 models

> hide #!3.4 models

> show #!3.1 models

> show #!3.2 models

> show #!3.3 models

> show #!3.4 models

> show #!3.5 models

> hide #!3.4 models

> hide #!3.3 models

> hide #!3.2 models

> hide #!3.1 models

> save /scratch2/jrai/mountpoint12tb/21may/Images/class3D_job039_class001.tiff

> hide #!3.5 models

> show #!3.4 models

> save /scratch2/jrai/mountpoint12tb/21may/Images/class3D_job039_class002.tiff

> hide #!3.4 models

> show #!3.3 models

> save /scratch2/jrai/mountpoint12tb/21may/Images/class3D_job039_class003.tiff

> hide #!3.3 models

> show #!3.2 models

> save /scratch2/jrai/mountpoint12tb/21may/Images/class3D_job039_class004.tiff

> hide #!3.2 models

> show #!3.1 models

> volume #3.1 level 0.001018

> save /scratch2/jrai/mountpoint12tb/21may/Images/class3D_job039_class005.tiff

> close #3.1-5

> close #3

> close #1

> open
> /scratch2/jrai/hpc_mountoint/jrai/21may22d/PostProcess/job052/postprocess.mrc

Opened postprocess.mrc as #1, grid size 256,256,256, pixel 1.07, shown at
level 0.0115, step 1, values float32  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 48992, resource id:
11010712, major code: 40 (TranslateCoords), minor code: 0  

> surface dust #2

> volume #1 level 0.01319

> surface undust

Missing or invalid "surfaces" argument: empty atom specifier  

> surface undust #1

> surface dust #1

> volume #1 level 0.004617

> volume #1 level 0.01295

> volume #1 level 0.008901

> volume #1 level 0.005807

> surface dust #1

> volume #1 level 0.01104

> save /scratch2/jrai/mountpoint12tb/21may/Images/pp_job052.tiff

> color #1 gray

> save /scratch2/jrai/mountpoint12tb/21may/Images/pp_job052.tiff

> close #1

> open
> /scratch2/jrai/mountpoint12tb/21may/P19/J151/cryosparc_P19_J151_class_02_00102_volume.mrc
> /scratch2/jrai/mountpoint12tb/21may/P19/J151/cryosparc_P19_J151_class_01_00102_volume.mrc
> /scratch2/jrai/mountpoint12tb/21may/P19/J151/cryosparc_P19_J151_class_00_00102_volume.mrc

Opened cryosparc_P19_J151_class_02_00102_volume.mrc as #1.1, grid size
128,128,128, pixel 2.15, shown at level 0.583, step 1, values float32  
Opened cryosparc_P19_J151_class_01_00102_volume.mrc as #1.2, grid size
128,128,128, pixel 2.15, shown at level 0.617, step 1, values float32  
Opened cryosparc_P19_J151_class_00_00102_volume.mrc as #1.3, grid size
128,128,128, pixel 2.15, shown at level 0.681, step 1, values float32  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 31565, resource id:
11018261, major code: 40 (TranslateCoords), minor code: 0  

> volume #1.1 level 0.5834

> volume #1.1 level 0.3244

> fitmap #group 1 in_map #2

Missing or invalid "atomsOrMap" argument: invalid objects specifier  

> fitmap #1.1 inMap #2

Fit map cryosparc_P19_J151_class_02_00102_volume.mrc in map
run_ct14_class001.mrc using 44317 points  
correlation = 0.8378, correlation about mean = 0.3813, overlap = 437.1  
steps = 148, shift = 3.68, angle = 12.7 degrees  
  
Position of cryosparc_P19_J151_class_02_00102_volume.mrc (#1.1) relative to
run_ct14_class001.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99555142 -0.02488321 -0.09087465 19.05868236  
0.01479670 0.99381863 -0.11002542 15.49379655  
0.09305071 0.10819132 0.98976573 -18.13420011  
Axis 0.75734292 -0.63833127 0.13771307  
Axis point 0.00000000 183.68491337 142.37342037  
Rotation angle (degrees) 8.28327388  
Shift along axis 2.04646702  
  

> fitmap #1.2 inMap #2

Fit map cryosparc_P19_J151_class_01_00102_volume.mrc in map
run_ct14_class001.mrc using 20969 points  
correlation = 0.8771, correlation about mean = 0.341, overlap = 359.4  
steps = 140, shift = 3.87, angle = 11.7 degrees  
  
Position of cryosparc_P19_J151_class_01_00102_volume.mrc (#1.2) relative to
run_ct14_class001.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99515919 -0.04477703 -0.08748257 21.35221386  
0.03383829 0.99186110 -0.12274575 15.02259506  
0.09226675 0.11919130 0.98857487 -18.49021696  
Axis 0.77671808 -0.57706972 0.25238771  
Axis point 0.00000000 174.09914329 126.11793630  
Rotation angle (degrees) 8.95989931  
Shift along axis 3.24886237  
  

> fitmap #1.3 inMap #2

Fit map cryosparc_P19_J151_class_00_00102_volume.mrc in map
run_ct14_class001.mrc using 20966 points  
correlation = 0.8807, correlation about mean = 0.3437, overlap = 398.7  
steps = 128, shift = 4.3, angle = 11.9 degrees  
  
Position of cryosparc_P19_J151_class_00_00102_volume.mrc (#1.3) relative to
run_ct14_class001.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99454544 -0.05773828 -0.08686572 24.09498810  
0.04820837 0.99297420 -0.10806565 10.56549857  
0.09249495 0.10328855 0.99034144 -17.27927847  
Axis 0.71220969 -0.60439967 0.35701316  
Axis point 0.00000000 193.58614204 110.94411937  
Rotation angle (degrees) 8.53301011  
Shift along axis 4.60597055  
  

> color #1 gray

> hide #!1.1 models

> hide #!1.2 models

> hide #!1.3 models

> show #!1.3 models

> volume #1.3 level 0.3866

> hide #!1.3 models

> show #!1.2 models

> volume #1.2 level 0.3959

> show #!1.3 models

> hide #!1.3 models

> hide #!1.1 models

> show #!1.1 models

> hide #!1 models

> show #!1 models

> show #!1.2 models

> hide #!1.1 models

> hide #!1.2 models

> show #!1.3 models

> hide #!1.3 models

> show #!1.2 models

> hide #!1.2 models

> show #!1.1 models

> show #!1.3 models

> show #!1.2 models

> hide #!1.1 models

> hide #!1.2 models

> hide #!1.3 models

> show #!1.1 models

> save /scratch2/jrai/mountpoint12tb/21may/Images/J151_class002.tiff

> hide #!1.1 models

> show #!1.2 models

> save /scratch2/jrai/mountpoint12tb/21may/Images/J151_class001.tiff

> hide #!1.2 models

> show #!1.3 models

> save /scratch2/jrai/mountpoint12tb/21may/Images/J151_class000.tiff

Traceback (most recent call last):  
File "/scratch/users/Jay/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
KeyboardInterrupt  
  
KeyboardInterrupt  
  
File "/scratch/users/Jay/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/scratch/users/Jay/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
KeyboardInterrupt  
  
KeyboardInterrupt  
  
File "/scratch/users/Jay/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/scratch/users/Jay/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
KeyboardInterrupt  
  
KeyboardInterrupt  
  
File "/scratch/users/Jay/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/scratch/users/Jay/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
KeyboardInterrupt  
  
KeyboardInterrupt  
  
File "/scratch/users/Jay/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/scratch/users/Jay/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
KeyboardInterrupt  
  
KeyboardInterrupt  
  
File "/scratch/users/Jay/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 460.32.03
OpenGL renderer: GeForce GTX 1080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUS
Model: All Series
OS: Ubuntu 16.04 xenial
Architecture: 64bit ELF
Virutal Machine: none
CPU: 16 Intel(R) Core(TM) i7-6900K CPU @ 3.20GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G        7.3G         23G        320M         31G         54G
	Swap:           15G        3.5G         12G

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:1b80] (rev a1)	
	Subsystem: ASUSTeK Computer Inc. Device [1043:859b]	
	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: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    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: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    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: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    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: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 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: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    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: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.2.0

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Component:	Unassigned → Input/Output
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Hung saving TIFF?

comment:2 by Tom Goddard, 4 years ago

Resolution:	→ can't reproduce
Status:	assigned → closed

User typed ctrl-C to the shell (Linux) where ChimeraX started generating a Python keyboard interrupt.

Was trying to save a tiff format image of the graphics. Was showing small maps (128 cube and 256 cube). The user had just successfully saved two tiff images, changed which map was shown and tried to save a third. Save was to what appears to be a mounted disk

/scratch2/jrai/mountpoint12tb/21may/Images/J151_class000.tiff

My guess is the save hung due to the disk not responding. Another less likely possibility is that the graphics rendering hung.

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