Opened 21 months ago

Closed 21 months ago

#14405 closed defect (fixed)

Quotes vs. semicolons

Reported by: olibclarke@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Command Line Version:
Keywords: Cc: pett, Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-14.2.1-arm64-arm-64bit
ChimeraX Version: 1.8.dev202401110052 (2024-01-11 00:52:34 UTC)
Description
I would like to make a command to reset my mouse modes to defaults (my defaults) after using one of the GUI right mouse modes.

To do this, I want to bind a series of commands to one of the buttons in the buttonpanel. The series of commands is:

mousemode alt right contour; mousemode right clip; mousemode alt left "translate selected models"; mousemode shift left "rotate selected models"; mousemode alt control left "pick blobs"

When I execute this, I get the following error:

mousemode alt leftMode "translate selected models"; mousemode shift left "rotate selected models"; mousemode alt control left "pick blobs"
Invalid "leftMode" argument: Should be one of 'bond rotation', 'center', 'center or translate', 'clip', 'clip rotate', 'contour level', 'create segmentations', 'crop volume', 'delete markers', 'distance', 'erase segmentations', 'identify object', 'label', 'link markers', 'map eraser', 'mark center', 'mark maximum', 'mark plane', 'mark point', 'mark surface', 'minimize', 'move label', 'move markers', 'move picked models', 'move planes', 'move segmentation cursor', 'next docked', 'none', 'pick blobs', 'pivot', 'play coordinates', 'play map series', 'resize markers', 'resize segmentation cursor', 'rotate', 'rotate and select', 'rotate independent', 'rotate selected atoms', 'rotate selected models', 'rotate slab', 'rotate z selected models', 'select', 'select add', 'select subtract', 'select toggle', 'swapaa', 'swipe as scroll', 'tape measure', 'toggle segmentation visibility', 'translate', 'translate selected atoms', 'translate selected models', 'translate xy selected models', 'tug', 'windowing', 'zone', or 'zoom'

But when I run any of the individual commands in the series, they work fine. Is this a bug, or if not what am I doing wrong?

Thanks (and sorry if I missed something obvious)

Cheers
Oli

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  

> camera ortho

> cofr centerOfView

> mousemode alt rightMode "contour level"

> mousemode rightMode clip

> mousemode alt leftMode "translate selected models"

> mousemode shift leftMode "rotate selected models"

> mousemode alt control leftMode "pick blobs"

> alias cofron cofr centerofview showpivot 7,0.25

> alias cofroff cofr centerofview showpivot false

> alias symclip cofr centerofview; clip near -$1 far $1 position cofr

> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; size stickradius 0.07; transparency 70;
> cofr centerofview; clip near -10 far 10 position cofr; color ##~num_residues
> cornflower blue

> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; style ions ball; size
> ballscale 0.2; size stickradius 0.07; cofr centerofview; clip near -10 far
> 10 position cofr; color ##~num_residues #3d60ffff; transparency 50

> alias project_map set bgColor black; lighting depthcue false; volume $1
> style image sdlevel 0,0 color white sdlevel 100,0.15 color white
> projectionmode 3d maximumIntensityProjection false dimTransparentVoxels
> false btcorrection true showOutlineBox false linearinterpolation true

> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1

> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1

> alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000;
> marker #10000 position cofr; sel ~sel; surface zone ##~num_residues
> nearAtoms sel distance 15; close #10000

> alias map_unsphere surface unzone ##~num_residues

> alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5;
> lighting soft

> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance 0; close #10000

> alias showmaps surface unzone ##~num_residues

> alias caps_off surface cap false

> alias caps_on surface cap true

> alias open_vseries "open browse vseries true"

> alias selbetween ks ri

> alias helix setattr $1 res is_helix true

> alias strand setattr $1 res is_strand true

> alias coil setattr $1 res is_strand false; setattr $1 res is_helix false

> alias rock_movie cofr showpivot false; movie record; rock y 30; wait 136;
> movie encode ~/Desktop/rock_movie.mp4; stop

> buttonpanel Shortcuts rows 3 columns 5

> buttonpanel Shortcuts add Vol_Viewer command "tool show 'Volume Viewer'"

> buttonpanel Shortcuts add Model_Panel command "tool show Models"

> buttonpanel Shortcuts add Log command "tool show Log"

> buttonpanel Shortcuts add default_disp command default_mol_display

> buttonpanel Shortcuts add map_sphere command map_sphere_15

> buttonpanel Shortcuts add map_unsphere command map_unsphere

> buttonpanel Shortcuts add cofron command cofron

> buttonpanel Shortcuts add cofroff command cofroff

> buttonpanel Shortcuts add cootmode command cootmode

> buttonpanel Shortcuts add mark_cofr command "marker #20000 position cofr"

> buttonpanel Shortcuts add hidemaps command hidemaps

> buttonpanel Shortcuts add showmaps command showmaps

> buttonpanel Shortcuts add reset_mouse command "mousemode alt right contour;
> mousemode right clip; mousemode alt left "translate selected models";
> mousemode shift left "rotate selected models"; mousemode alt control left
> "pick blobs""

> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true

Saved volume settings  
UCSF ChimeraX version: 1.8.dev202401110052 (2024-01-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/oc2188/Downloads/cryosparc_P30_J1194_00108_volume_series/J1194_class_73_00108_volume.mrc
> format mrc

Opened J1194_class_73_00108_volume.mrc as #1, grid size 48,48,48, pixel 5.21,
shown at level 0.32, step 1, values float32  

> ui mousemode right "translate selected models"

> mousemode alt rightMode "contour level"

> mousemode rightMode clip

> mousemode alt leftMode "translate selected models"; mousemode shift left
> "rotate selected models"; mousemode alt control left "pick blobs"

Invalid "leftMode" argument: Should be one of 'bond rotation', 'center',
'center or translate', 'clip', 'clip rotate', 'contour level', 'create
segmentations', 'crop volume', 'delete markers', 'distance', 'erase
segmentations', 'identify object', 'label', 'link markers', 'map eraser',
'mark center', 'mark maximum', 'mark plane', 'mark point', 'mark surface',
'minimize', 'move label', 'move markers', 'move picked models', 'move planes',
'move segmentation cursor', 'next docked', 'none', 'pick blobs', 'pivot',
'play coordinates', 'play map series', 'resize markers', 'resize segmentation
cursor', 'rotate', 'rotate and select', 'rotate independent', 'rotate selected
atoms', 'rotate selected models', 'rotate slab', 'rotate z selected models',
'select', 'select add', 'select subtract', 'select toggle', 'swapaa', 'swipe
as scroll', 'tape measure', 'toggle segmentation visibility', 'translate',
'translate selected atoms', 'translate selected models', 'translate xy
selected models', 'tug', 'windowing', 'zone', or 'zoom'  

> tool show Log

> mousemode alt rightMode "contour level"

> mousemode rightMode clip

> mousemode alt leftMode "translate selected models"; mousemode shift left
> "rotate selected models"; mousemode alt control left "pick blobs"

Invalid "leftMode" argument: Should be one of 'bond rotation', 'center',
'center or translate', 'clip', 'clip rotate', 'contour level', 'create
segmentations', 'crop volume', 'delete markers', 'distance', 'erase
segmentations', 'identify object', 'label', 'link markers', 'map eraser',
'mark center', 'mark maximum', 'mark plane', 'mark point', 'mark surface',
'minimize', 'move label', 'move markers', 'move picked models', 'move planes',
'move segmentation cursor', 'next docked', 'none', 'pick blobs', 'pivot',
'play coordinates', 'play map series', 'resize markers', 'resize segmentation
cursor', 'rotate', 'rotate and select', 'rotate independent', 'rotate selected
atoms', 'rotate selected models', 'rotate slab', 'rotate z selected models',
'select', 'select add', 'select subtract', 'select toggle', 'swapaa', 'swipe
as scroll', 'tape measure', 'toggle segmentation visibility', 'translate',
'translate selected atoms', 'translate selected models', 'translate xy
selected models', 'tug', 'windowing', 'zone', or 'zoom'  

> mousemode alt rightMode "contour level"

> mousemode rightMode clip

> mousemode alt leftMode "translate selected models"; mousemode shift left
> "rotate selected models"; mousemode alt control left "pick blobs"

Invalid "leftMode" argument: Should be one of 'bond rotation', 'center',
'center or translate', 'clip', 'clip rotate', 'contour level', 'create
segmentations', 'crop volume', 'delete markers', 'distance', 'erase
segmentations', 'identify object', 'label', 'link markers', 'map eraser',
'mark center', 'mark maximum', 'mark plane', 'mark point', 'mark surface',
'minimize', 'move label', 'move markers', 'move picked models', 'move planes',
'move segmentation cursor', 'next docked', 'none', 'pick blobs', 'pivot',
'play coordinates', 'play map series', 'resize markers', 'resize segmentation
cursor', 'rotate', 'rotate and select', 'rotate independent', 'rotate selected
atoms', 'rotate selected models', 'rotate slab', 'rotate z selected models',
'select', 'select add', 'select subtract', 'select toggle', 'swapaa', 'swipe
as scroll', 'tape measure', 'toggle segmentation visibility', 'translate',
'translate selected atoms', 'translate selected models', 'translate xy
selected models', 'tug', 'windowing', 'zone', or 'zoom'  

> mousemode alt rightMode "contour level"

> mousemode rightMode clip

> mousemode alt leftMode "translate selected models"; mousemode shift left
> "rotate selected models"; mousemode alt control left "pick blobs"

Invalid "leftMode" argument: Should be one of 'bond rotation', 'center',
'center or translate', 'clip', 'clip rotate', 'contour level', 'create
segmentations', 'crop volume', 'delete markers', 'distance', 'erase
segmentations', 'identify object', 'label', 'link markers', 'map eraser',
'mark center', 'mark maximum', 'mark plane', 'mark point', 'mark surface',
'minimize', 'move label', 'move markers', 'move picked models', 'move planes',
'move segmentation cursor', 'next docked', 'none', 'pick blobs', 'pivot',
'play coordinates', 'play map series', 'resize markers', 'resize segmentation
cursor', 'rotate', 'rotate and select', 'rotate independent', 'rotate selected
atoms', 'rotate selected models', 'rotate slab', 'rotate z selected models',
'select', 'select add', 'select subtract', 'select toggle', 'swapaa', 'swipe
as scroll', 'tape measure', 'toggle segmentation visibility', 'translate',
'translate selected atoms', 'translate selected models', 'translate xy
selected models', 'tug', 'windowing', 'zone', or 'zoom'  

> mousemode alt rightMode "contour level"

> mousemode rightMode clip

> mousemode alt leftMode "translate selected models"; mousemode shift left
> "rotate selected models"; mousemode alt control left "pick blobs"

Invalid "leftMode" argument: Should be one of 'bond rotation', 'center',
'center or translate', 'clip', 'clip rotate', 'contour level', 'create
segmentations', 'crop volume', 'delete markers', 'distance', 'erase
segmentations', 'identify object', 'label', 'link markers', 'map eraser',
'mark center', 'mark maximum', 'mark plane', 'mark point', 'mark surface',
'minimize', 'move label', 'move markers', 'move picked models', 'move planes',
'move segmentation cursor', 'next docked', 'none', 'pick blobs', 'pivot',
'play coordinates', 'play map series', 'resize markers', 'resize segmentation
cursor', 'rotate', 'rotate and select', 'rotate independent', 'rotate selected
atoms', 'rotate selected models', 'rotate slab', 'rotate z selected models',
'select', 'select add', 'select subtract', 'select toggle', 'swapaa', 'swipe
as scroll', 'tape measure', 'toggle segmentation visibility', 'translate',
'translate selected atoms', 'translate selected models', 'translate xy
selected models', 'tug', 'windowing', 'zone', or 'zoom'  

> mousemode alt rightMode "contour level"

> mousemode rightMode clip

> mousemode alt leftMode "translate selected models"; mousemode shift left
> "rotate selected models"; mousemode alt control left "pick blobs"

Invalid "leftMode" argument: Should be one of 'bond rotation', 'center',
'center or translate', 'clip', 'clip rotate', 'contour level', 'create
segmentations', 'crop volume', 'delete markers', 'distance', 'erase
segmentations', 'identify object', 'label', 'link markers', 'map eraser',
'mark center', 'mark maximum', 'mark plane', 'mark point', 'mark surface',
'minimize', 'move label', 'move markers', 'move picked models', 'move planes',
'move segmentation cursor', 'next docked', 'none', 'pick blobs', 'pivot',
'play coordinates', 'play map series', 'resize markers', 'resize segmentation
cursor', 'rotate', 'rotate and select', 'rotate independent', 'rotate selected
atoms', 'rotate selected models', 'rotate slab', 'rotate z selected models',
'select', 'select add', 'select subtract', 'select toggle', 'swapaa', 'swipe
as scroll', 'tape measure', 'toggle segmentation visibility', 'translate',
'translate selected atoms', 'translate selected models', 'translate xy
selected models', 'tug', 'windowing', 'zone', or 'zoom'  

> mousemode alt rightMode "contour level"

> mousemode rightMode clip

> mousemode alt leftMode "translate selected models"; mousemode shift left
> "rotate selected models"; mousemode alt control left "pick blobs"

Invalid "leftMode" argument: Should be one of 'bond rotation', 'center',
'center or translate', 'clip', 'clip rotate', 'contour level', 'create
segmentations', 'crop volume', 'delete markers', 'distance', 'erase
segmentations', 'identify object', 'label', 'link markers', 'map eraser',
'mark center', 'mark maximum', 'mark plane', 'mark point', 'mark surface',
'minimize', 'move label', 'move markers', 'move picked models', 'move planes',
'move segmentation cursor', 'next docked', 'none', 'pick blobs', 'pivot',
'play coordinates', 'play map series', 'resize markers', 'resize segmentation
cursor', 'rotate', 'rotate and select', 'rotate independent', 'rotate selected
atoms', 'rotate selected models', 'rotate slab', 'rotate z selected models',
'select', 'select add', 'select subtract', 'select toggle', 'swapaa', 'swipe
as scroll', 'tape measure', 'toggle segmentation visibility', 'translate',
'translate selected atoms', 'translate selected models', 'translate xy
selected models', 'tug', 'windowing', 'zone', or 'zoom'  

> mousemode alt rightMode "contour level"

> mousemode rightMode clip

> mousemode alt leftMode "translate selected models"

> mousemode alt rightMode "contour level"

> mousemode rightMode clip

> mousemode alt leftMode "translate selected models"; mousemode shift left
> "rotate selected models"

Invalid "leftMode" argument: Should be one of 'bond rotation', 'center',
'center or translate', 'clip', 'clip rotate', 'contour level', 'create
segmentations', 'crop volume', 'delete markers', 'distance', 'erase
segmentations', 'identify object', 'label', 'link markers', 'map eraser',
'mark center', 'mark maximum', 'mark plane', 'mark point', 'mark surface',
'minimize', 'move label', 'move markers', 'move picked models', 'move planes',
'move segmentation cursor', 'next docked', 'none', 'pick blobs', 'pivot',
'play coordinates', 'play map series', 'resize markers', 'resize segmentation
cursor', 'rotate', 'rotate and select', 'rotate independent', 'rotate selected
atoms', 'rotate selected models', 'rotate slab', 'rotate z selected models',
'select', 'select add', 'select subtract', 'select toggle', 'swapaa', 'swipe
as scroll', 'tape measure', 'toggle segmentation visibility', 'translate',
'translate selected atoms', 'translate selected models', 'translate xy
selected models', 'tug', 'windowing', 'zone', or 'zoom'  

> mousemode alt rightMode "contour level"

> mousemode rightMode clip

> mousemode alt leftMode "translate selected models"; mousemode alt control
> left "pick blobs"

Invalid "leftMode" argument: Should be one of 'bond rotation', 'center',
'center or translate', 'clip', 'clip rotate', 'contour level', 'create
segmentations', 'crop volume', 'delete markers', 'distance', 'erase
segmentations', 'identify object', 'label', 'link markers', 'map eraser',
'mark center', 'mark maximum', 'mark plane', 'mark point', 'mark surface',
'minimize', 'move label', 'move markers', 'move picked models', 'move planes',
'move segmentation cursor', 'next docked', 'none', 'pick blobs', 'pivot',
'play coordinates', 'play map series', 'resize markers', 'resize segmentation
cursor', 'rotate', 'rotate and select', 'rotate independent', 'rotate selected
atoms', 'rotate selected models', 'rotate slab', 'rotate z selected models',
'select', 'select add', 'select subtract', 'select toggle', 'swapaa', 'swipe
as scroll', 'tape measure', 'toggle segmentation visibility', 'translate',
'translate selected atoms', 'translate selected models', 'translate xy
selected models', 'tug', 'windowing', 'zone', or 'zoom'  

> mousemode alt rightMode "contour level"

> mousemode rightMode clip

> mousemode alt leftMode "translate selected models"

> mousemode alt rightMode "contour level"

> mousemode rightMode clip

> mousemode alt leftMode "translate selected models"; mousemode shift left
> "rotate selected models"

Invalid "leftMode" argument: Should be one of 'bond rotation', 'center',
'center or translate', 'clip', 'clip rotate', 'contour level', 'create
segmentations', 'crop volume', 'delete markers', 'distance', 'erase
segmentations', 'identify object', 'label', 'link markers', 'map eraser',
'mark center', 'mark maximum', 'mark plane', 'mark point', 'mark surface',
'minimize', 'move label', 'move markers', 'move picked models', 'move planes',
'move segmentation cursor', 'next docked', 'none', 'pick blobs', 'pivot',
'play coordinates', 'play map series', 'resize markers', 'resize segmentation
cursor', 'rotate', 'rotate and select', 'rotate independent', 'rotate selected
atoms', 'rotate selected models', 'rotate slab', 'rotate z selected models',
'select', 'select add', 'select subtract', 'select toggle', 'swapaa', 'swipe
as scroll', 'tape measure', 'toggle segmentation visibility', 'translate',
'translate selected atoms', 'translate selected models', 'translate xy
selected models', 'tug', 'windowing', 'zone', or 'zoom'  

> mousemode alt rightMode "contour level"

> mousemode rightMode clip

> mousemode alt leftMode "translate selected models""

Invalid "leftMode" argument: Should be one of 'bond rotation', 'center',
'center or translate', 'clip', 'clip rotate', 'contour level', 'create
segmentations', 'crop volume', 'delete markers', 'distance', 'erase
segmentations', 'identify object', 'label', 'link markers', 'map eraser',
'mark center', 'mark maximum', 'mark plane', 'mark point', 'mark surface',
'minimize', 'move label', 'move markers', 'move picked models', 'move planes',
'move segmentation cursor', 'next docked', 'none', 'pick blobs', 'pivot',
'play coordinates', 'play map series', 'resize markers', 'resize segmentation
cursor', 'rotate', 'rotate and select', 'rotate independent', 'rotate selected
atoms', 'rotate selected models', 'rotate slab', 'rotate z selected models',
'select', 'select add', 'select subtract', 'select toggle', 'swapaa', 'swipe
as scroll', 'tape measure', 'toggle segmentation visibility', 'translate',
'translate selected atoms', 'translate selected models', 'translate xy
selected models', 'tug', 'windowing', 'zone', or 'zoom'  

> mousemode alt rightMode "contour level"

> mousemode rightMode clip

> mousemode alt leftMode "translate selected models"

> mousemode alt rightMode "contour level"

> mousemode rightMode clip

> mousemode alt leftMode "translate selected models"; mousemode shift left
> "rotate selected models"; mousemode alt control left "pick blobs"

Invalid "leftMode" argument: Should be one of 'bond rotation', 'center',
'center or translate', 'clip', 'clip rotate', 'contour level', 'create
segmentations', 'crop volume', 'delete markers', 'distance', 'erase
segmentations', 'identify object', 'label', 'link markers', 'map eraser',
'mark center', 'mark maximum', 'mark plane', 'mark point', 'mark surface',
'minimize', 'move label', 'move markers', 'move picked models', 'move planes',
'move segmentation cursor', 'next docked', 'none', 'pick blobs', 'pivot',
'play coordinates', 'play map series', 'resize markers', 'resize segmentation
cursor', 'rotate', 'rotate and select', 'rotate independent', 'rotate selected
atoms', 'rotate selected models', 'rotate slab', 'rotate z selected models',
'select', 'select add', 'select subtract', 'select toggle', 'swapaa', 'swipe
as scroll', 'tape measure', 'toggle segmentation visibility', 'translate',
'translate selected atoms', 'translate selected models', 'translate xy
selected models', 'tug', 'windowing', 'zone', or 'zoom'  

> mousemode alt rightMode "contour level"

> mousemode rightMode clip

> mousemode alt leftMode "translate selected models"; mousemode shift left
> 'rotate selected models'; mousemode alt control left 'pick blobs'

Invalid "leftMode" argument: incomplete quoted text  

> mousemode alt rightMode "contour level"

> mousemode rightMode clip

> mousemode alt leftMode "translate selected models"; mousemode shift left
> 'rotate selected models'; mousemode alt control left 'pick blobs'

Invalid "leftMode" argument: incomplete quoted text  

> mousemode alt rightMode "contour level"

> mousemode rightMode clip

> mousemode alt leftMode "translate selected models"

> mousemode shift leftMode "rotate selected models"; mousemode alt control
> left "pick blobs"

Invalid "leftMode" argument: Should be one of 'bond rotation', 'center',
'center or translate', 'clip', 'clip rotate', 'contour level', 'create
segmentations', 'crop volume', 'delete markers', 'distance', 'erase
segmentations', 'identify object', 'label', 'link markers', 'map eraser',
'mark center', 'mark maximum', 'mark plane', 'mark point', 'mark surface',
'minimize', 'move label', 'move markers', 'move picked models', 'move planes',
'move segmentation cursor', 'next docked', 'none', 'pick blobs', 'pivot',
'play coordinates', 'play map series', 'resize markers', 'resize segmentation
cursor', 'rotate', 'rotate and select', 'rotate independent', 'rotate selected
atoms', 'rotate selected models', 'rotate slab', 'rotate z selected models',
'select', 'select add', 'select subtract', 'select toggle', 'swapaa', 'swipe
as scroll', 'tape measure', 'toggle segmentation visibility', 'translate',
'translate selected atoms', 'translate selected models', 'translate xy
selected models', 'tug', 'windowing', 'zone', or 'zoom'  

> mousemode shift leftMode "rotate selected models"

> mousemode alt control leftMode "pick blobs"

> mousemode alt rightMode "contour level"

> mousemode rightMode clip

> mousemode alt leftMode "translate selected models"; mousemode shift left
> "rotate selected models"; mousemode alt control left "pick blobs"

Invalid "leftMode" argument: Should be one of 'bond rotation', 'center',
'center or translate', 'clip', 'clip rotate', 'contour level', 'create
segmentations', 'crop volume', 'delete markers', 'distance', 'erase
segmentations', 'identify object', 'label', 'link markers', 'map eraser',
'mark center', 'mark maximum', 'mark plane', 'mark point', 'mark surface',
'minimize', 'move label', 'move markers', 'move picked models', 'move planes',
'move segmentation cursor', 'next docked', 'none', 'pick blobs', 'pivot',
'play coordinates', 'play map series', 'resize markers', 'resize segmentation
cursor', 'rotate', 'rotate and select', 'rotate independent', 'rotate selected
atoms', 'rotate selected models', 'rotate slab', 'rotate z selected models',
'select', 'select add', 'select subtract', 'select toggle', 'swapaa', 'swipe
as scroll', 'tape measure', 'toggle segmentation visibility', 'translate',
'translate selected atoms', 'translate selected models', 'translate xy
selected models', 'tug', 'windowing', 'zone', or 'zoom'  

> mousemode alt rightMode "contour level"

> mousemode rightMode clip

> mousemode alt leftMode "translate selected models"; mousemode shift left
> "rotate selected models"; mousemode alt control left "pick blobs"

Invalid "leftMode" argument: Should be one of 'bond rotation', 'center',
'center or translate', 'clip', 'clip rotate', 'contour level', 'create
segmentations', 'crop volume', 'delete markers', 'distance', 'erase
segmentations', 'identify object', 'label', 'link markers', 'map eraser',
'mark center', 'mark maximum', 'mark plane', 'mark point', 'mark surface',
'minimize', 'move label', 'move markers', 'move picked models', 'move planes',
'move segmentation cursor', 'next docked', 'none', 'pick blobs', 'pivot',
'play coordinates', 'play map series', 'resize markers', 'resize segmentation
cursor', 'rotate', 'rotate and select', 'rotate independent', 'rotate selected
atoms', 'rotate selected models', 'rotate slab', 'rotate z selected models',
'select', 'select add', 'select subtract', 'select toggle', 'swapaa', 'swipe
as scroll', 'tape measure', 'toggle segmentation visibility', 'translate',
'translate selected atoms', 'translate selected models', 'translate xy
selected models', 'tug', 'windowing', 'zone', or 'zoom'  

> mousemode alt rightMode "contour level"

> mousemode rightMode clip

> mousemode alt leftMode "translate selected models"; mousemode shift left
> "rotate selected models"; mousemode alt control left "pick blobs"

Invalid "leftMode" argument: Should be one of 'bond rotation', 'center',
'center or translate', 'clip', 'clip rotate', 'contour level', 'create
segmentations', 'crop volume', 'delete markers', 'distance', 'erase
segmentations', 'identify object', 'label', 'link markers', 'map eraser',
'mark center', 'mark maximum', 'mark plane', 'mark point', 'mark surface',
'minimize', 'move label', 'move markers', 'move picked models', 'move planes',
'move segmentation cursor', 'next docked', 'none', 'pick blobs', 'pivot',
'play coordinates', 'play map series', 'resize markers', 'resize segmentation
cursor', 'rotate', 'rotate and select', 'rotate independent', 'rotate selected
atoms', 'rotate selected models', 'rotate slab', 'rotate z selected models',
'select', 'select add', 'select subtract', 'select toggle', 'swapaa', 'swipe
as scroll', 'tape measure', 'toggle segmentation visibility', 'translate',
'translate selected atoms', 'translate selected models', 'translate xy
selected models', 'tug', 'windowing', 'zone', or 'zoom'  

> mousemode shift leftMode "rotate selected models"

> mousemode alt rightMode "contour level"

> mousemode rightMode clip

> mousemode alt leftMode "translate selected models"; mousemode shift left
> "rotate selected models"; mousemode alt control left "pick blobs"

Invalid "leftMode" argument: Should be one of 'bond rotation', 'center',
'center or translate', 'clip', 'clip rotate', 'contour level', 'create
segmentations', 'crop volume', 'delete markers', 'distance', 'erase
segmentations', 'identify object', 'label', 'link markers', 'map eraser',
'mark center', 'mark maximum', 'mark plane', 'mark point', 'mark surface',
'minimize', 'move label', 'move markers', 'move picked models', 'move planes',
'move segmentation cursor', 'next docked', 'none', 'pick blobs', 'pivot',
'play coordinates', 'play map series', 'resize markers', 'resize segmentation
cursor', 'rotate', 'rotate and select', 'rotate independent', 'rotate selected
atoms', 'rotate selected models', 'rotate slab', 'rotate z selected models',
'select', 'select add', 'select subtract', 'select toggle', 'swapaa', 'swipe
as scroll', 'tape measure', 'toggle segmentation visibility', 'translate',
'translate selected atoms', 'translate selected models', 'translate xy
selected models', 'tug', 'windowing', 'zone', or 'zoom'  

> tool show Log




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,5
      Model Number: Z17J00171LL/A
      Chip: Apple M2 Max
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 64 GB
      System Firmware Version: 10151.61.4
      OS Loader Version: 10151.61.4

Software:

    System Software Overview:

      System Version: macOS 14.2.1 (23C71)
      Kernel Version: Darwin 23.2.0
      Time since boot: 10 days, 5 hours, 33 minutes

Graphics/Displays:

    Apple M2 Max:

      Chipset Model: Apple M2 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 30
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.15
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.3
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.52
    ChimeraX-AtomicLibrary: 12.1.4
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.11
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8.dev202401110052
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.9
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.15
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NMRSTAR: 1.0.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.2.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.1
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.14.2
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.5
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.0
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynmrstar: 3.3.2
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (5)

comment:1 by pett, 21 months ago

Cc: pett Tom Goddard added
Component: Unassigned → Command Line
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Quotes vs. semicolons

Hi Oli,

This is an issue with the command parsing. It is parsing left to right, so when it hits the first double quote, it looks for a matching double quote that is immediately followed by white space or end-of-line. The double quote you intend to end the command is immediately followed by a semicolon, not white space. So the simple workaround is to put spaces both before and after the semicolons in your command sequence.
I think Greg can fix the command parsing to allow semicolons directly after quotes to separate commands.

--Eric

comment:2 by olibclarke@…, 21 months ago 

Ok thanks Eric, so that fixes the string of commands (if I run separately), but if I run it at startup it still fails - this is the line in my startup:

buttonpanel Shortcuts add reset_mouse command "mousemode alt right contour ; mousemode right clip ; mousemode alt left "translate selected models" ; mousemode shift left "rotate selected models" ; mousemode alt control left "pick blobs""

Is this still a parsing issue? maybe if I replace the "inner" double quotes with single quotes?

Cheers
Oli

comment:3 by olibclarke@…, 21 months ago 

Ok that was indeed the issue - if I leave the outer double quotes around the command string, but replace all the inner mousemode double quotes with single quotes, then it works! Thanks!

Cheers
Oli

comment:4 by pett, 21 months ago

Yes, that is still a parsing issue, and not one that can be fixed in the parser. As you found out, the "outer" quotes need to be a different type from the "inner" quotes.

comment:5 by Greg Couch, 21 months ago

Resolution: → fixed
Status: assigned → closed

Fixed in tomorrow's daily build.

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