Opened 6 years ago

Closed 6 years ago

#2945 closed defect (fixed)

Crash opening 6bb5 on Windows

Reported by: goddard@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 0.93 (2020-03-11)
Description
"open 6bb5" causes immediate crash on Windows.
Several other structures 1a0m, 4hus, 4v6x do not cause a crash.
6bb5 does not cause a crash Mac.


Log:
UCSF ChimeraX version: 0.93 (2020-03-11)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 442.19
OpenGL renderer: GeForce GTX 1080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Gigabyte Technology Co., Ltd.
Model: Z270X-Gaming K7
OS: Microsoft Windows 10 Home (Build 18362)
Memory: 17,129,693,184
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-7700K CPU @ 4.20GHz"

Change History (5)

in reply to:  1 ; comment:1 by goddard@…, 6 years ago 

Actually opening 4hus also causes a crash on windows about half the time.  But 1a0m and 4v6x always seem to open without crashing.

Also on my older Feb 21 Windows ChimeraX these crashes do not occur.

comment:2 by Tom Goddard, 6 years ago

Platform: → all
Project: → ChimeraX

Here is debug output to the shell indicating a crash in apply_auto_styling().

Initializing core
C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\win32\lib\pywintypes.py:2: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses

import imp, sys, os

Toolshed: init False False None
Toolshed: cache dir: C:\Users\goddard\AppData\Local\UCSF\ChimeraX\Cache\0.93\toolshed
Toolshed: site dir: C:\Users\goddard\AppData\Local\UCSF\ChimeraX\0.93\site-packages
Toolshed: loading bundles
Toolshed: build available bundle ChimeraX_RMF 0.5
Toolshed: build available bundle ChimeraX_RMF 0.5
Toolshed: build available bundle ChimeraX_RMF 0.5
Toolshed: build available bundle ChimeraX_RMF 0.4
Toolshed: build available bundle ChimeraX_RMF 0.4
Toolshed: build available bundle ChimeraX_RMF 0.4
Toolshed: build available bundle ChimeraX_RMF 0.3
Toolshed: build available bundle ChimeraX_RMF 0.3
Toolshed: build available bundle ChimeraX_RMF 0.3
Toolshed: build available bundle ChimeraX_RealSense 1.3
Toolshed: build available bundle ChimeraX_RMF 0.2
Toolshed: build available bundle ChimeraX_RMF 0.2
Toolshed: build available bundle ChimeraX_RMF 0.2
Toolshed: build available bundle ChimeraX_RMF 0.1
Toolshed: build available bundle ChimeraX_RMF 0.1
Toolshed: build available bundle ChimeraX_RMF 0.1
Toolshed: build available bundle ChimeraX_RealSense 1.2
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b4.dev2
Toolshed: build available bundle ChimeraX_Clipper 0.11.1
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b4.dev2
Toolshed: build available bundle ChimeraX_Clipper 0.11.1
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b4.dev2
Toolshed: build available bundle ChimeraX_Clipper 0.11.1
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b4.dev1
Toolshed: build available bundle ChimeraX_Clipper 0.11.0
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b4.dev1
Toolshed: build available bundle ChimeraX_Clipper 0.11.0
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b4.dev1
Toolshed: build available bundle ChimeraX_Clipper 0.11.0
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b4.dev0
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b4.dev0
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b4.dev0
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b4
Toolshed: build available bundle ChimeraX_Clipper 0.10.0
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b4
Toolshed: build available bundle ChimeraX_Clipper 0.10.0
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b4
Toolshed: build available bundle ChimeraX_Clipper 0.10.0
Toolshed: build available bundle ChimeraX_RealSense 1.1
Toolshed: build available bundle ChimeraX_RealSense 1.0
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev8
Toolshed: build available bundle ChimeraX_Clipper 0.9.12
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev8
Toolshed: build available bundle ChimeraX_Clipper 0.9.12
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev8
Toolshed: build available bundle ChimeraX_Clipper 0.9.12
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev7
Toolshed: build available bundle ChimeraX_Clipper 0.9.11
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev7
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev7
Toolshed: build available bundle ChimeraX_Clipper 0.9.11
Toolshed: build available bundle ChimeraX_Clipper 0.9.11
Toolshed: build available bundle ChimeraX_Maestro 1.5
Toolshed: build available bundle ChimeraX_Maestro 1.4
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev6
Toolshed: build available bundle ChimeraX_Clipper 0.9.10
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev6
Toolshed: build available bundle ChimeraX_Clipper 0.9.10
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev6
Toolshed: build available bundle ChimeraX_Clipper 0.9.10
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev5
Toolshed: build available bundle ChimeraX_Clipper 0.9.9
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev5
Toolshed: build available bundle ChimeraX_Clipper 0.9.9
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev5
Toolshed: build available bundle ChimeraX_Clipper 0.9.9
Toolshed: build available bundle ChimeraX_Maestro 1.3
Toolshed: build available bundle ChimeraX_Maestro 1.2
Toolshed: build available bundle ChimeraX_Maestro 1.1
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev4
Toolshed: build available bundle ChimeraX_Clipper 0.9.8
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev4
Toolshed: build available bundle ChimeraX_Clipper 0.9.8
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev4
Toolshed: build available bundle ChimeraX_Clipper 0.9.8
Toolshed: build available bundle ChimeraX_Maestro 1.0
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev3
Toolshed: build available bundle ChimeraX_Clipper 0.9.7
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev3
Toolshed: build available bundle ChimeraX_Clipper 0.9.7
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev3
Toolshed: build available bundle ChimeraX_Clipper 0.9.7
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev2
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev2
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev2
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev1
Toolshed: build available bundle ChimeraX_Clipper 0.9.6
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev1
Toolshed: build available bundle ChimeraX_Clipper 0.9.6
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev1
Toolshed: build available bundle ChimeraX_Clipper 0.9.6
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev0
Toolshed: build available bundle ChimeraX_Clipper 0.9.5
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev0
Toolshed: build available bundle ChimeraX_Clipper 0.9.5
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev0
Toolshed: build available bundle ChimeraX_Clipper 0.9.5
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3
Toolshed: build available bundle ChimeraX_Clipper 0.9.4
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3
Toolshed: build available bundle ChimeraX_Clipper 0.9.4
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3
Toolshed: build available bundle ChimeraX_Clipper 0.9.4
Toolshed: build available bundle ChimeraX_Clipper 0.9.3
Toolshed: build available bundle ChimeraX_Clipper 0.9.3
Toolshed: build available bundle ChimeraX_Clipper 0.9.2
Toolshed: build available bundle ChimeraX_Clipper 0.9.2
Toolshed: build available bundle ChimeraX_Clipper 0.9.1
Toolshed: build available bundle ChimeraX_Clipper 0.9.1
Toolshed: build available bundle ChimeraX_Clipper 0.9.1
Toolshed: build available bundle ChimeraX_Clipper 0.9
Toolshed: build available bundle ChimeraX_Clipper 0.9
Toolshed: build available bundle ChimeraX_Clipper 0.9
Toolshed: build available bundle MolecularDynamicsViewer 1.1
Toolshed: build available bundle MolecularDynamicsViewer 1.0
Toolshed: build available bundle ChimeraX_Clipper 0.4.0
Toolshed: build available bundle ChimeraX_Clipper 0.3.1
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b2
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b2
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b2
Toolshed: build available bundle ChimeraX_Clipper 0.3
Toolshed: build available bundle ChimeraX_Clipper 0.3
Toolshed: build available bundle ChimeraX_Clipper 0.3
Toolshed: build available bundle ChimeraX_Clipper 0.2.1
Toolshed: build available bundle ChimeraX_Clipper 0.2.1
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b1
Toolshed: build available bundle ChimeraX_Clipper 0.2.0
Toolshed: build available bundle ChimeraX_ISOLDE 1.0b1
Toolshed: build available bundle ChimeraX_Clipper 0.2.0
Toolshed: build available bundle ChimeraX_Tempy 0.6.0
Toolshed: build available bundle ChimeraX_Tempy 0.5.0
Toolshed: build available bundle ChimeraX_Tempy 0.4.0
Toolshed: build available bundle ChimeraX_Tempy 0.3.0
Toolshed: build available bundle ChimeraX_SignalViewer 1.0
Toolshed: build available bundle ChimeraX_Tempy 0.2.0
Toolshed: build available bundle ChimeraX_Tempy 0.1.0
Toolshed: build available bundle ChimeraX_Tempy 0.0.5
Toolshed: build available bundle ChimeraX_Tempy 0.0.4
Toolshed: build available bundle ChimeraX_Tempy 0.0.3
Toolshed: build available bundle ChimeraX_Tempy 0.0.2
Toolshed: build available bundle ChimeraX_Tempy 0.0.1
Toolshed: build available bundle ChimeraX_Stringdb 0.1
Toolshed: build available bundle ChimeraX_Cytoscape 0.1
Toolshed: reload False False
Toolshed: _bundle_cache False
Toolshed: InstalledBundleCache.load: rebuild_cache False
Toolshed: InstalledBundleCache._read_cache: C:\Users\goddard\AppData\Local\UCSF\ChimeraX\Cache\0.93\toolshed\bundle_info.cache
Toolshed: _is_cache_newer
Toolshed: InstalledBundleCache._read_cache: 111 bundles
Toolshed: InstalledBundleCache.load: using cached data
Toolshed: register bundle ChimeraX-Core 0.93
Toolshed: register bundle ChimeraX-Rotamer-Lib-Mgr 1.0
Toolshed: register bundle ChimeraX-Movie 1.0
Toolshed: delay_registration movie
Toolshed: register bundle ChimeraX-Scheme-Mgr 1.0
Toolshed: register bundle ChimeraX-Segment 1.0
Toolshed: delay_registration segmentation
Toolshed: register bundle ChimeraX-Geometry 1.0
Toolshed: register bundle ChimeraX-VTK 1.0
Toolshed: register_file_type VTK PolyData
Toolshed: register bundle ChimeraX-WavefrontOBJ 1.0
Toolshed: register_file_type Wavefront OBJ
Toolshed: register bundle ChimeraX-RestServer 0.1
Toolshed: delay_registration remotecontrol rest
Toolshed: register bundle ChimeraX-Test 1.0
Toolshed: delay_registration debug test
Toolshed: delay_registration debug exectest
Toolshed: delay_registration debug expectfail
Toolshed: register bundle ChimeraX-SDF 1.0
Toolshed: register_file_type MDL MOL/SDF
Toolshed: register bundle ChimeraX-MLP 1.0
Toolshed: delay_registration mlp
Toolshed: register bundle ChimeraX-List-Info 0.1
Toolshed: delay_registration info
Toolshed: register bundle ChimeraX-SmoothLines 1.0
Toolshed: delay_registration smoothlines
Toolshed: register bundle ChimeraX-RemoteControl 1.0
Toolshed: delay_registration remotecontrol xmlrpc
Toolshed: register bundle ChimeraX-Preset-Mgr 1.0
Toolshed: delay_registration preset
Toolshed: register bundle ChimeraX-ExperimentalCommands 1.0
Toolshed: delay_registration ribbon
Toolshed: delay_registration ribbon hide
Toolshed: delay_registration ~ribbon
Toolshed: delay_registration getcrd
Toolshed: delay_registration debug dumpspec
Toolshed: register bundle ChimeraX-Storm 1.0
Toolshed: register_file_type STORM
Toolshed: register bundle ChimeraX-WebServices 1.0
Toolshed: register bundle ChimeraX-STL 1.0
Toolshed: register_file_type StereoLithography
Toolshed: register bundle ChimeraX-Morph 1.0
Toolshed: delay_registration morph
Toolshed: register bundle ChimeraX-Struts 1.0
Toolshed: delay_registration struts
Toolshed: register bundle ChimeraX-RotamerLibs-Richardson 1.0
Toolshed: register bundle ChimeraX-RotamerLibs-Dynameomics 1.0
Toolshed: register bundle ChimeraX-Crystal 1.0
Toolshed: register bundle ChimeraX-gltf 1.0
Toolshed: register_file_type glTF
Toolshed: register bundle ChimeraX-CellPack 1.0
Toolshed: register_file_type cellpack
Toolshed: register bundle ChimeraX-Graphics 1.0
Toolshed: register bundle ChimeraX-Dicom 1.0
Toolshed: register bundle ChimeraX-RotamerLibs-Dunbrack 1.0
Toolshed: register bundle ChimeraX-SpaceNavigator 1.0
Toolshed: delay_registration device snav
Toolshed: register bundle ChimeraX-MapData 1.0
Toolshed: register bundle ChimeraX-Texture 1.0
Toolshed: delay_registration texture
Toolshed: register bundle ChimeraX-MouseModes 1.0
Toolshed: delay_registration ui mousemode
Toolshed: delay_registration mousemode
Toolshed: register bundle ChimeraX-ColorGlobe 1.0
Toolshed: register_file_type Directional FSC
Toolshed: register bundle ChimeraX-Atomic 1.0
Toolshed: register bundle ChimeraX-Vive 1.1
Toolshed: delay_registration vr
Toolshed: delay_registration device vr
Toolshed: register bundle ChimeraX-Read-Pbonds 1.0
Toolshed: register_file_type Pseudobonds
Toolshed: register bundle ChimeraX-PDB 1.0
Toolshed: register_file_type PDB
Toolshed: register bundle ChimeraX-Dssp 1.0
Toolshed: register bundle ChimeraX-UI 1.0
Toolshed: delay_registration ui
Toolshed: register bundle ChimeraX-MD-crds 1.0
Toolshed: register_file_type Gromacs full-precision coordinates
Toolshed: register_file_type Gromacs compressed coordinates
Toolshed: register_file_type DCD coordinates
Toolshed: register bundle ChimeraX-ChemGroup 1.0
Toolshed: register bundle ChimeraX-Std-Commands 1.0
Toolshed: delay_registration alias
Toolshed: delay_registration alias list
Toolshed: delay_registration alias delete
Toolshed: delay_registration ~alias
Toolshed: delay_registration align
Toolshed: delay_registration camera
Toolshed: delay_registration cartoon
Toolshed: delay_registration ~cartoon
Toolshed: delay_registration cd
Toolshed: delay_registration clip
Toolshed: delay_registration ~clip
Toolshed: delay_registration close
Toolshed: delay_registration cofr
Toolshed: delay_registration ~cofr
Toolshed: delay_registration color
Toolshed: delay_registration colour
Toolshed: delay_registration color delete
Toolshed: delay_registration color list
Toolshed: delay_registration color name
Toolshed: delay_registration color show
Toolshed: delay_registration colordef
Toolshed: delay_registration ~colordef
Toolshed: delay_registration colourdef
Toolshed: delay_registration ~colourdef
Toolshed: delay_registration coordset
Toolshed: delay_registration crossfade
Toolshed: delay_registration delete
Toolshed: delay_registration dssp
Toolshed: delay_registration exit
Toolshed: delay_registration quit
Toolshed: delay_registration graphics
Toolshed: delay_registration hide
Toolshed: delay_registration ~show
Toolshed: delay_registration ~display
Toolshed: delay_registration lighting
Toolshed: delay_registration lighting model
Toolshed: delay_registration material
Toolshed: delay_registration measure buriedarea
Toolshed: delay_registration measure center
Toolshed: delay_registration measure convexity
Toolshed: delay_registration measure inertia
Toolshed: delay_registration measure length
Toolshed: delay_registration measure symmetry
Toolshed: delay_registration move
Toolshed: delay_registration palette
Toolshed: delay_registration pdbimages
Toolshed: delay_registration perframe
Toolshed: delay_registration ~perframe
Toolshed: delay_registration pwd
Toolshed: delay_registration rainbow
Toolshed: delay_registration rename
Toolshed: delay_registration roll
Toolshed: delay_registration runscript
Toolshed: delay_registration select
Toolshed: delay_registration ~select
Toolshed: delay_registration set
Toolshed: delay_registration ~set
Toolshed: delay_registration setattr
Toolshed: delay_registration show
Toolshed: delay_registration display
Toolshed: delay_registration size
Toolshed: delay_registration split
Toolshed: delay_registration stop
Toolshed: delay_registration style
Toolshed: delay_registration sym
Toolshed: delay_registration tile
Toolshed: delay_registration time
Toolshed: delay_registration transparency
Toolshed: delay_registration turn
Toolshed: delay_registration undo
Toolshed: delay_registration redo
Toolshed: delay_registration usage
Toolshed: delay_registration version
Toolshed: delay_registration view
Toolshed: delay_registration wait
Toolshed: delay_registration windowsize
Toolshed: delay_registration select zone
Toolshed: delay_registration zoom
Toolshed: register bundle ChimeraX-Dist-Monitor 1.0
Toolshed: delay_registration distance
Toolshed: delay_registration ~distance
Toolshed: register bundle ChimeraX-Smiles 1.0
Toolshed: register_file_type SMILES
Toolshed: register bundle ChimeraX-PubChem 1.0
Toolshed: register bundle ChimeraX-Atom-Search 1.0
Toolshed: register bundle ChimeraX-Registration 0.1
Toolshed: delay_registration registration status
Toolshed: register bundle ChimeraX-ButtonPanel 1.0
Toolshed: delay_registration buttonpanel
Toolshed: register bundle ChimeraX-Help 0.9a1
Toolshed: delay_registration help
Toolshed: register_file_type HTML
Toolshed: register bundle ChimeraX-Contacts 1.0
Toolshed: delay_registration interfaces
Toolshed: register bundle ChimeraX-ModelPanel 1.0
Toolshed: register bundle ChimeraX-mmCIF 1.1
Toolshed: register_file_type mmCIF
Toolshed: register bundle ChimeraX-ShowAttr 1.0
Toolshed: register bundle ChimeraX-FunctionKey 1.0
Toolshed: delay_registration ui functionkey
Toolshed: delay_registration functionkey
Toolshed: register bundle ChimeraX-SwapAA 1.0
Toolshed: delay_registration swapaa mousemode
Toolshed: register bundle ChimeraX-PickBlobs 1.0
Toolshed: delay_registration measure blob
Toolshed: register bundle ChimeraX-Shortcuts 1.0
Toolshed: delay_registration ks
Toolshed: register bundle ChimeraX-Shell 1.0
Toolshed: register bundle ChimeraX-SwapRes 1.0
Toolshed: delay_registration swapaa
Toolshed: register bundle ChimeraX-Zone 1.0
Toolshed: delay_registration zone
Toolshed: register bundle ChimeraX-SideView 1.0
Toolshed: register bundle ChimeraX-Connect-Structure 1.0
Toolshed: register bundle ChimeraX-MedicalToolbar 1.0
Toolshed: register bundle ChimeraX-Bug-Reporter 1.0
Toolshed: register bundle ChimeraX-BondRot 1.0
Toolshed: delay_registration torsion
Toolshed: register bundle ChimeraX-BasicActions 0.1
Toolshed: delay_registration name
Toolshed: delay_registration name frozen
Toolshed: delay_registration name delete
Toolshed: delay_registration name list
Toolshed: register bundle ChimeraX-CommandLine 1.0
Toolshed: register bundle ChimeraX-Clashes 1.0
Toolshed: delay_registration clashes
Toolshed: delay_registration contacts
Toolshed: delay_registration ~clashes
Toolshed: delay_registration ~contacts
Toolshed: register bundle ChimeraX-Markers 1.0
Toolshed: delay_registration marker
Toolshed: register_file_type Marker model
Toolshed: register bundle ChimeraX-MapEraser 1.0
Toolshed: delay_registration volume erase
Toolshed: register bundle ChimeraX-TapeMeasure 1.0
Toolshed: register bundle ChimeraX-Dist-UI 1.0
Toolshed: register bundle ChimeraX-Hbonds 1.0
Toolshed: delay_registration hbonds
Toolshed: delay_registration ~hbonds
Toolshed: register bundle ChimeraX-Meeting 1.0
Toolshed: delay_registration meeting
Toolshed: delay_registration meeting close
Toolshed: delay_registration meeting send
Toolshed: delay_registration conference
Toolshed: delay_registration conference set
Toolshed: delay_registration conference close
Toolshed: delay_registration conference send
Toolshed: register bundle ChimeraX-ResidueFit 1.0
Toolshed: delay_registration resfit
Toolshed: register bundle ChimeraX-Mol2 1.0
Toolshed: register_file_type Sybyl Mol2
Toolshed: register bundle ChimeraX-Label 1.0
Toolshed: delay_registration 2dlabels
Toolshed: delay_registration label
Toolshed: delay_registration ~label
Toolshed: register bundle ChimeraX-Log 1.0
Toolshed: delay_registration echo
Toolshed: delay_registration log
Toolshed: register bundle ChimeraX-VolumeMenu 1.0
Toolshed: register bundle ChimeraX-ModelSeries 1.0
Toolshed: delay_registration mseries
Toolshed: register bundle ChimeraX-Map 1.0
Toolshed: delay_registration volume
Toolshed: delay_registration vop
Toolshed: delay_registration molmap
Toolshed: delay_registration measure mapstats
Toolshed: register bundle ChimeraX-Alignments 1.0
Toolshed: delay_registration sequence
Toolshed: register_file_type FASTA
Toolshed: register_file_type MSF
Toolshed: register_file_type PIR
Toolshed: register_file_type ALN
Toolshed: register_file_type HSSP
Toolshed: register_file_type Pfam
Toolshed: register_file_type RSF
Toolshed: register_file_type Stockholm
Toolshed: register bundle ChimeraX-FileHistory 1.0
Toolshed: register bundle ChimeraX-Segger 1.0
Toolshed: register bundle ChimeraX-Tug 1.0
Toolshed: register bundle ChimeraX-MMTF 1.0
Toolshed: register_file_type MMTF
Toolshed: register bundle ChimeraX-Toolbar 0.1
Toolshed: register bundle ChimeraX-AddH 1.0
Toolshed: delay_registration addh
Toolshed: register bundle ChimeraX-AlignmentAlgorithms 1.0
Toolshed: register bundle ChimeraX-Mask 1.0
Toolshed: delay_registration volume mask
Toolshed: delay_registration volume onesmask
Toolshed: register bundle ChimeraX-Modeller 1.0
Toolshed: delay_registration modeller comparative
Toolshed: delay_registration modeller scores
Toolshed: register bundle ChimeraX-MapFit 1.0
Toolshed: delay_registration fitmap
Toolshed: register bundle ChimeraX-IHM 1.0
Toolshed: register_file_type IHM
Toolshed: register bundle ChimeraX-Surface 1.0
Toolshed: delay_registration color electrostatic
Toolshed: delay_registration color sample
Toolshed: delay_registration color gradient
Toolshed: delay_registration color radial
Toolshed: delay_registration color cylindrical
Toolshed: delay_registration color height
Toolshed: delay_registration surface
Toolshed: delay_registration ~surface
Toolshed: delay_registration surface show
Toolshed: delay_registration surface hide
Toolshed: delay_registration surface close
Toolshed: delay_registration surface style
Toolshed: delay_registration surface cap
Toolshed: delay_registration surface dust
Toolshed: delay_registration surface undust
Toolshed: delay_registration surface zone
Toolshed: delay_registration surface unzone
Toolshed: delay_registration surface check
Toolshed: delay_registration sop
Toolshed: delay_registration volume splitbyzone
Toolshed: delay_registration measure sasa
Toolshed: delay_registration measure volume
Toolshed: delay_registration measure area
Toolshed: register_file_type Collada
Toolshed: register bundle ChimeraX-AlignmentHdrs 1.0
Toolshed: register bundle ChimeraX-AlignmentMatrices 1.0
Toolshed: register bundle ChimeraX-Bumps 1.0
Toolshed: delay_registration bumps
Toolshed: delay_registration cbumps
Toolshed: register bundle ChimeraX-ViewDockX 0.1
Toolshed: delay_registration viewdockx
Toolshed: delay_registration viewdockx down
Toolshed: delay_registration viewdockx up
Toolshed: register_file_type mol2
Toolshed: register_file_type pdbqt
Toolshed: register bundle ChimeraX-Crosslinks 1.0
Toolshed: delay_registration crosslinks
Toolshed: register bundle ChimeraX-Cage-Builder 1.0
Toolshed: delay_registration cage
Toolshed: register bundle ChimeraX-BlastProtein 0.2
Toolshed: delay_registration blastprotein
Toolshed: delay_registration blastprotein mav
Toolshed: delay_registration blastpdb
Toolshed: register bundle ChimeraX-uniprot 1.0
Toolshed: register_file_type UniProt
Toolshed: register bundle ChimeraX-MapSeries 1.0
Toolshed: delay_registration vseries
Toolshed: delay_registration measure motion
Toolshed: register bundle ChimeraX-MapFilter 1.0
Toolshed: register bundle ChimeraX-SeqView 1.0
Toolshed: register bundle ChimeraX-BILD 0.2
Toolshed: register_file_type BILD
Toolshed: register bundle ChimeraX-BuildStructure 1.0
Toolshed: delay_registration build
Toolshed: register bundle ChimeraX-Nucleotides 0.1
Toolshed: delay_registration nucleotides
Toolshed: delay_registration ~nucleotides
Toolshed: register bundle ChimeraX-MatchMaker 1.0
Toolshed: delay_registration matchmaker
Toolshed: delay_registration mmaker
Toolshed: finished loading bundles
Initializing bundles
Toolshed: initialize_bundles False
Toolshed: initialize manager rotamers for bundle 'ChimeraX-Rotamer-Lib-Mgr'
Toolshed: initialize manager url_schemes for bundle 'ChimeraX-Scheme-Mgr'
Toolshed: initialize manager presets for bundle 'ChimeraX-Preset-Mgr'
Toolshed: initialize manager alignments for bundle 'ChimeraX-Alignments'
Toolshed: initialize manager toolbar for bundle 'ChimeraX-Toolbar'
Toolshed: find_bundle ChimeraX-Toolbar True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Nucleotides True None
Toolshed: find_bundle ChimeraX-Nucleotides True None
Toolshed: find_bundle ChimeraX-Nucleotides True None
Toolshed: find_bundle ChimeraX-Nucleotides True None
Toolshed: find_bundle ChimeraX-Nucleotides True None
Toolshed: initialize manager start structure for bundle 'ChimeraX-BuildStructure'
Toolshed: custom initialization for bundle 'ChimeraX-RestServer'
Toolshed: custom initialization for bundle 'ChimeraX-Dicom'
Toolshed: custom initialization for bundle 'ChimeraX-MouseModes'
Toolshed: custom initialization for bundle 'ChimeraX-Atomic'
Toolshed: custom initialization for bundle 'ChimeraX-Vive'
Toolshed: custom initialization for bundle 'ChimeraX-ChemGroup'
Toolshed: custom initialization for bundle 'ChimeraX-Std-Commands'
Toolshed: custom initialization for bundle 'ChimeraX-Dist-Monitor'
Toolshed: custom initialization for bundle 'ChimeraX-Registration'
Toolshed: custom initialization for bundle 'ChimeraX-Help'
Toolshed: custom initialization for bundle 'ChimeraX-FunctionKey'
Toolshed: custom initialization for bundle 'ChimeraX-SwapAA'
Toolshed: custom initialization for bundle 'ChimeraX-PickBlobs'
Toolshed: custom initialization for bundle 'ChimeraX-Zone'
Toolshed: custom initialization for bundle 'ChimeraX-Bug-Reporter'
Toolshed: custom initialization for bundle 'ChimeraX-BondRot'
Toolshed: custom initialization for bundle 'ChimeraX-BasicActions'
Toolshed: custom initialization for bundle 'ChimeraX-CommandLine'
Toolshed: custom initialization for bundle 'ChimeraX-Markers'
Toolshed: custom initialization for bundle 'ChimeraX-MapEraser'
Toolshed: custom initialization for bundle 'ChimeraX-TapeMeasure'
Toolshed: custom initialization for bundle 'ChimeraX-Dist-UI'
Toolshed: custom initialization for bundle 'ChimeraX-Label'
Toolshed: custom initialization for bundle 'ChimeraX-Log'
Toolshed: custom initialization for bundle 'ChimeraX-VolumeMenu'
Toolshed: custom initialization for bundle 'ChimeraX-Map'
Toolshed: custom initialization for bundle 'ChimeraX-Segger'
Toolshed: custom initialization for bundle 'ChimeraX-Tug'
Toolshed: custom initialization for bundle 'ChimeraX-Surface'
Toolshed: custom initialization for bundle 'ChimeraX-ViewDockX'
Toolshed: custom initialization for bundle 'ChimeraX-MapSeries'
Starting main interface
Toolshed: find_bundle ChimeraX-Toolbar True None
Toolshed: find_bundle ChimeraX-Toolbar True None
Toolshed: find_bundle ChimeraX-Toolbar True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Toolshed: find_bundle ChimeraX-Shortcuts True None
Finished initialization
Windows fatal exception: code 0xc0000374

Thread 0x00002084 (most recent call first):

File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\threading.py", line 300 in wait
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\threading.py", line 552 in wait
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\threading.py", line 1175 in run
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\threading.py", line 926 in _bootstrap_inner
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\threading.py", line 890 in _bootstrap

Current thread 0x00000454 (most recent call first):

File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\chimerax\atomic\molarray.py", line 237 in filter
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\chimerax\atomic\structure.py", line 2343 in apply_auto_styling
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\chimerax\atomic\structure.py", line 125 in added_to_session
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\chimerax\atomic\structure.py", line 2263 in added_to_session
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\chimerax\core\models.py", line 588 in add
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\chimerax\core\commands\open.py", line 160 in _fetch_from_database
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\chimerax\core\commands\open.py", line 44 in open
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2845 in run
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\chimerax\core\commands\run.py", line 31 in run
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line 445 in cxcmd
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line 429 in defer
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\chimerax\ui\gui.py", line 610 in customEvent
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\chimerax\ui\gui.py", line 268 in event_loop
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\ChimeraX_main.py", line 772 in init
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\site-packages\ChimeraX_main.py", line 904 in <module>
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\runpy.py", line 85 in _run_code
File "C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin\lib\runpy.py", line 193 in _run_module_as_main

$

comment:3 by Tom Goddard, 6 years ago

Component: Unassigned → Core
Owner: set to Tom Goddard
Status: new → assigned

Appears to be a bug in find_close_points() probably introduced by my change from long to int64_t.

comment:4 by Tom Goddard, 6 years ago

Summary: ChimeraX bug report submission → Crash opening 6bb5 on Windows

comment:5 by Tom Goddard, 6 years ago

Resolution: → fixed
Status: assigned → closed

Fixed.

New code that produce a numpy array from a C++ vector<int64_t> was pretending long was 64-bits, writing off the end of the numpy array. I made it properly fill a long array (32-bit on Windows).

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