"alias usage" interfering with the actual alias

[olibclarke@…]

The following bug report has been submitted:
Platform:        macOS-15.6-arm64-arm-64bit
ChimeraX Version: 1.11.dev202507251829 (2025-07-25 18:29:55 UTC)
Description

Hi,

I'm testing out the "usage" command for aliases, and I've run into what seems to be a bug.

I have the following alias saved in my preferences:

alias local_fitmap ~sel; close #10000-10001; marker #10000 position cofr; sel #10000; volume zone $2 nearAtoms sel range $3 newMap true modelid 10001 minimalbounds true; fitmap $1 inmap #10001 eachmodel true; close #10001; close sel; show $2

This takes either a model or a map, zones it using a certain radius and uses the zone to fit the model/map to a target map. I run it like this:

local_fitmap #1 #2 20

Where the three arguments are two model IDs and a zone radius. This all works fine. But if I run it after saving the following usage command in the preferences (on the line following the alias definition) then it won't run - it complains there are not enough arguments:

alias usage local_fitmap synopsis "Fits the selected model or map to the target map, using a zone around the center of rotation for fitting." $1 "model to fit" $2 "map to fit to" $3 "Radius of local zone"

The usage command seems fine - when I run "usage local_fitmap" I get the expected info printed to the log - but it is somehow interfering with the alias it is describing. Am I doing something obviously stupid (likely), or is this a bug of some kind?

Cheers
Oli

Log:
> runscript /Users/oc2188/Dropbox/chimera_startup/chimerax_startup.py

> 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 volume unzone ~##num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; volume zone ~##num_residues nearAtoms sel
> minimalBounds true range 15; close #10000

> alias cubic_map shape sphere radius $1 modelid #10000; volume onesmask
> #10000 spacing 1 border -0.5

> alias map_unsphere volume unzone ~##num_residues

> alias fit_by_chain split $1; fitmap $1.* inmap $2 eachmodel true; combine
> $1.* close true

> 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 local_fitmap ~sel; close #10000-10001; marker #10000 position cofr;
> sel #10000; volume zone $2 nearAtoms sel range $3 newMap true modelid 10001
> minimalbounds true; fitmap $1 inmap #10001 eachmodel true; close #10001;
> close sel; show $2

> alias usage local_fitmap synopsis "Fits the selected model or map to the
> target map, using a zone around the center of rotation for fitting." $1
> "model to fit" $2 "map to fit to" $3 "Radius of local zone"

> 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 50; wait 600;
> movie encode ~/Desktop/rock_movie.mp4; stop

> alias centersel cofr sel; clip near 10 position cofr; clip far -10 position
> cofr; cofr centerOfView showpivot true; view sel

> functionkey F1 prevmodel

> functionkey F2 nextmodel

> functionkey F3 centersel

> functionkey F4 view all

> 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
> radius 1"

> buttonpanel Shortcuts add hidemaps command hidemaps

> buttonpanel Shortcuts add showmaps command showmaps

> buttonpanel Shortcuts add reset_mouse_and_help 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'; help https://github.com/olibclarke/chimerax-
> trimmings/blob/main/default_mousemodes.md"

> buttonpanel Shortcuts add previous_model command prevmodel

> buttonpanel Shortcuts add next_model command nextmodel

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

Saved volume settings  
UCSF ChimeraX version: 1.11.dev202507251829 (2025-07-25)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/oc2188/Downloads/9NYD.cif format mmcif

Summary of feedback from opening /Users/oc2188/Downloads/9NYD.cif  
---  
warning | Unable to fetch template for 'A1B94': will use incomplete information in mmCIF file  
  
9NYD.cif title:  
Cryo-EM structure of the glycosyltransferase GtrB in the pre-catalysis and
product-bound state [more info...]  
  
Chain information for 9NYD.cif #1  
---  
Chain | Description | UniProt  
A B C D | Glycosyltransferase sll0501 | Y501_SYNY3 2-318  
  
Non-standard residues in 9NYD.cif #1  
---  
5TR —
[(2~{E},6~{E},10~{E},14~{E},18~{Z},22~{E},26~{Z},30~{E},34~{E},38~{E})-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,14,18,22,26,30,34,38,42-undecaenyl]
dihydrogen phosphate (Undecaprenyl phosphate)  
A1B94 — undecaprenyl phosphate-glucose  
MG — magnesium ion  
UDP — uridine-5'-diphosphate  
UPG — uridine-5'-diphosphate-glucose (uridine-5'-monophosphate glucopyranosyl-
monophosphate ester)  
  

> open /Users/oc2188/Downloads/9NYD_map.mrc format mrc

Opened 9NYD_map.mrc as #2, grid size 256,256,256, pixel 0.83, shown at level
0.164, step 1, values float32  

> cootmode

> surface cap false

Changed 10396 atom styles  
Changed 4 atom styles  
Changed 0 atom styles  
Changed 1 ball scales  
Changed 10640 bond radii  

> cofron

> local_fitmap #1 #2 20

Not enough arguments  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
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: 11881.140.96
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.6 (24G84)
      Kernel Version: Darwin 24.6.0
      Time since boot: 7 hours, 19 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:
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    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    babel: 2.17.0
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    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
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    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
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    ChimeraX-AlphaFold: 1.0.1
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    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.10
    ChimeraX-AtomicLibrary: 14.1.21
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    ChimeraX-Boltz: 1.1
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    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
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    ChimeraX-ChemGroup: 2.0.2
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    ChimeraX-ColorGlobe: 1.0
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    ChimeraX-CommandLine: 1.3.0
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    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11.dev202507251829
    ChimeraX-CoreFormats: 1.2
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    ChimeraX-Crystal: 1.0
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    ChimeraX-DataFormats: 1.2.4
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    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 1.4.1
    ChimeraX-Hbonds: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
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    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
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    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
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    ChimeraX-MDcrds: 2.14
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    ChimeraX-Meeting: 1.0.1
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    ChimeraX-Mol2: 2.0.3
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    ChimeraX-Morph: 1.0.2
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    ChimeraX-MutationScores: 1.0
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    ChimeraX-PubChem: 2.2
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    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
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    ChimeraX-SelInspector: 1.0
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    ChimeraX-ShowSequences: 1.0.3
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    ChimeraX-Smiles: 2.1.2
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    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
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    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.47
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.1
    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
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    tzdata: 2025.2
    urllib3: 2.5.0
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[Greg Couch]

Probably a bug. Investigating.

[Greg Couch]

Fixed in [develop 233e6b940].