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~/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 [email protected]           
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