Example crashed VMD (MacOS)
stenczelt opened this issue · comments
Dear developers, I have tried to take a look at the example given, with a freshly installed VMD version and sadly it just crashed the program. I am not sure if this is an issue with VMD itself, or the given input file is broken.
OS: MacOS Big Sur 11.1 (Mac Book Pro 13" 2020)
VMD version: 1.9.4a51-x86_64-Rev9 (currently only intel+bigsur version from website with tag: (Dec 21, 2020): MacOS X Big Sur fixes w/ Tcl/Tk 8.6.11)
The output is the following:
~/work/nanoreactor/example master ❯ vmd -e reactions.vmd -args coors.xyz х KILL 9s Py wfl_test 08:19:12 am
Info) VMD for MACOSXX86_64, version 1.9.4a51 (December 21, 2020)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd@ks.uiuc.edu
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 8 CPUs detected.
Info) CPU features: SSE2 SSE4.1 AVX AVX2 FMA F16 HT
Info) High-DPI OpenGL display support enabled.
Info) OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
Info) Features: STENCIL MDE MTX NPOT PP PS GLSL(OVF)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (16384x16384), 3-D (2048x2048x2048), Multitexture (8)
usage: mol <command> [args...]
Molecules and Data:
new [file name] [options...] -- load file into a new molecule
new atoms <natoms> -- generate a new molecule with 'empty' atoms
addfile <file name> [options...] -- load files into existing molecule
options: type, first, last, step, waitfor, volsets, filebonds, autobonds,
<molid> (addfile only)
load <file type> <file name> -- load molecule (obsolescent)
urlload <file type> <URL> -- load molecule from URL
pdbload <four letter accession id> -- download molecule from the PDB
cancel <molid> -- cancel load/save of trajectory
delete <molid> -- delete given molecule
rename <molid> <name> -- Rename the specified molecule
dataflag <molid> [set | unset] <flagname> -- Set/unset data output flags
list [all|<molid>] -- displays info about molecules
Molecule GUI Properties:
top <molid> -- make that molecule 'top'
on <molid> -- make molecule visible
off <molid> -- make molecule invisible
fix <molid> -- don't apply mouse motions
free <molid> -- let mouse move molecules
active <molid> -- make molecule active
inactive <molid> -- make molecule inactive
Graphical Representations:
addrep <molid> -- add a new representation
delrep <repid> <molid> -- delete rep
default [color | style | selection | material] <value>
representation|rep <style> -- set the drawing style for new reps
selection <selection> -- set the selection for new reps
color <color> -- set the color for new reps
material <material> -- set the material for new reps
modstyle <repid> <molid> <style> -- change the drawing style for a rep
modselect <repid> <molid> <selection> -- change the selection for a rep
modcolor <repid> <molid> <color> -- change the color for a rep
modmaterial <repid> <molid> <material> -- change the material for a rep
repname <molid> <repid> -- Get the name of a rep
repindex <molid> <repname> -- Get the repid of a rep from its name
reanalyze <molid> -- Re-analyze structure after changes
bondsrecalc <molid> -- Recalculate bonds, current timestep
ssrecalc <molid> -- Recalculate secondary structure (Cartoon)
selupdate <repid> <molid> [on|off] -- Get/Set auto recalc of rep selection
colupdate <repid> <molid> [on|off] -- Get/Set auto recalc of rep color
scaleminmax <molid> <repid> [<min> <max>|auto] -- Get/set colorscale minmax
drawframes <molid> <repid> [<framespec>|now] -- Get/Set drawn frame range
smoothrep <molid> <repid> [smooth] -- Get or set trajectory smoothing value
showperiodic <molid> <repid> [flags] -- Get or set periodic image display
numperiodic <molid> <repid> <n> -- Get or set number of periodic images
showrep <molid> <repid> [on|off] -- Turn selected rep on or off
volaxes <molid> <volID> <Xaxis> <Yaxis> <Zaxis> -- set vol axes
voldelete <molid> <volID> -- delete volumetric data
volmove <molid> <volID> <matrix> -- transform volumetric data
volorigin <molid> <volID> <vector> -- set origin
volscale <molid> <volID> <vector> -- scale volume
Clipping Planes:
clipplane center <clipid> <repid> <molid> [<vector>]
clipplane color <clipid> <repid> <molid> [<vector>]
clipplane normal <clipid> <repid> <molid> [<vector>]
clipplane status <clipid> <repid> <molid> [<mode>]
clipplane num
See also the molinfo command
Usage: Either launch VMD with 'vmd -e test.vmd -args my_xyz_file.xyz'
or open VMD and run 'play my_xyz_file.xyz'
coors.xyz
Info) Using plugin xyz for structure file coors.xyz
Info) Using plugin xyz for coordinates from file coors.xyz
Info) Finished with coordinate file coors.xyz.
Info) Analyzing structure ...
Info) Atoms: 228
Info) Bonds: 0
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 228
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 228 Protein: 0 Nucleic: 0
0
atomselect0
228
0
color.dat
couldn't open "color.dat": no such file or directory
1510
0
can't read "fp": no such variable
can't read "fp": no such variable
0
bonds.dat
couldn't open "bonds.dat": no such file or directory
can't read "fp": no such variable
charge.dat
can't read "fp": no such variable
spin.dat
can't read "fp": no such variable
0
vmd > 2021-01-25 08:19:49.096 VMD[2916:181886] -[FLWindow tkLayoutChanged]: unrecognized selector sent to instance 0x7f8c4544eb00
2021-01-25 08:19:49.104 VMD[2916:181886] *** Terminating app due to uncaught exception 'NSInvalidArgumentException', reason: '-[FLWindow tkLayoutChanged]: unrecognized selector sent to instance 0x7f8c4544eb00'
*** First throw call stack:
(
0 CoreFoundation 0x00007fff204936af __exceptionPreprocess + 242
1 libobjc.A.dylib 0x00007fff201cb3c9 objc_exception_throw + 48
2 CoreFoundation 0x00007fff20515c85 -[NSObject(NSObject) __retain_OA] + 0
3 CoreFoundation 0x00007fff203fb07d ___forwarding___ + 1467
4 CoreFoundation 0x00007fff203faa38 _CF_forwarding_prep_0 + 120
5 CoreFoundation 0x00007fff2040efec __CFNOTIFICATIONCENTER_IS_CALLING_OUT_TO_AN_OBSERVER__ + 12
6 CoreFoundation 0x00007fff204aa89b ___CFXRegistrationPost_block_invoke + 49
7 CoreFoundation 0x00007fff204aa80f _CFXRegistrationPost + 454
8 CoreFoundation 0x00007fff203dfbde _CFXNotificationPost + 723
9 Foundation 0x00007fff2114eabe -[NSNotificationCenter postNotificationName:object:userInfo:] + 59
10 AppKit 0x00007fff23756caa -[NSWindow(NSFullScreen) _didEnterFullScreen] + 118
11 AppKit 0x00007fff2313fd7f -[_NSWindowEnterFullScreenTransitionController doAfterEnterFullScreen] + 266
12 AppKit 0x00007fff235a817c -[_NSEnterFullScreenTransitionController _performFinalTransitionCleanup] + 50
13 AppKit 0x00007fff235a80ff __68-[_NSEnterFullScreenTransitionController _startFullScreenTransition]_block_invoke + 225
14 libdispatch.dylib 0x00007fff201755dd _dispatch_call_block_and_release + 12
15 libdispatch.dylib 0x00007fff201767c7 _dispatch_client_callout + 8
16 libdispatch.dylib 0x00007fff20182b86 _dispatch_main_queue_callback_4CF + 940
17 CoreFoundation 0x00007fff20456970 __CFRUNLOOP_IS_SERVICING_THE_MAIN_DISPATCH_QUEUE__ + 9
18 CoreFoundation 0x00007fff20418852 __CFRunLoopRun + 2731
19 CoreFoundation 0x00007fff204176ce CFRunLoopRunSpecific + 563
20 HIToolbox 0x00007fff2869c6d0 RunCurrentEventLoopInMode + 292
21 HIToolbox 0x00007fff2869c4cc ReceiveNextEventCommon + 709
22 HIToolbox 0x00007fff2869c1ef _BlockUntilNextEventMatchingListInModeWithFilter + 64
23 AppKit 0x00007fff22c34de9 _DPSNextEvent + 883
24 AppKit 0x00007fff22c335af -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1366
25 Tk 0x0000000106cfec57 Tk_MacOSXSetupTkNotifier + 355
26 Tcl 0x0000000106e3bb35 Tcl_DoOneEvent + 238
27 VMD 0x0000000104f208fa _ZN13TclTextInterp10doTkUpdateEv + 14
28 VMD 0x0000000104ecbec1 _ZN6UIText11check_eventEv + 47
29 VMD 0x0000000104e253f5 _ZN12CommandQueue12check_eventsEv + 41
30 VMD 0x0000000104ecebb8 _ZN6VMDApp9VMDupdateEi + 38
31 VMD 0x0000000104f038b9 main + 176
32 libdyld.dylib 0x00007fff2033c621 start + 1
)
libc++abi.dylib: terminating with uncaught exception of type NSException
[1] 2916 abort -e reactions.vmd -args coors.xyz
I think I have realised what the problem was, the installation of nanoreactor was not complete.