Color zone "far color" arg problem

[rposert@…]

The following bug report has been submitted:
Platform:        macOS-14.6.1-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Using `color zone` with `sharp true` and `far` set to a color (named or hex; anything except "keep") throws a ValueError. It seems to still color the surface...

To reproduce:
1) Open any volume (#1)
2) Open any model (#2)
3) Run `color zone #1 near #2 sharp true far blue`

Log:
> open /Users/rposert/.chimerax-config/init.cxc

> open ui.cxc

> ui mousemode right zoom

> style stick

Changed 0 atom styles  

> cofr centerOfView

> graphics selection color blue width 6

executed ui.cxc  

> open oli.cxc

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

Saved volume settings  

> alias map_sphere surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance $1; close #10000

> alias map_unsphere surface unzone ##~num_residues

executed oli.cxc  

> open color.cxc

> volume defaultvalues initialColors #0077BB,#EE7733,#EE3377,#009988,#CC3311

> color name icol1 #0077BB

Color 'icol1' is opaque: rgb(0%, 46.7%, 73.3%) hex: #0077bb

  

> color name icol2 #EE7733

Color 'icol2' is opaque: rgb(93.3%, 46.7%, 20%) hex: #ee7733

  

> color name icol3 #EE3377

Color 'icol3' is opaque: rgb(93.3%, 20%, 46.7%) hex: #ee3377

  

> color name icol4 #009988

Color 'icol4' is opaque: rgb(0%, 60%, 53.3%) hex: #009988

  

> color name icol5 #CC3311

Color 'icol5' is opaque: rgb(80%, 20%, 6.67%) hex: #cc3311

  

> color name lcol1 #6ECAFF

Color 'lcol1' is opaque: rgb(43.1%, 79.2%, 100%) hex: #6ecaff

  

> color name lcol2 #FFA36E

Color 'lcol2' is opaque: rgb(100%, 63.9%, 43.1%) hex: #ffa36e

  

> color name lcol3 #ED8CB0

Color 'lcol3' is opaque: rgb(92.9%, 54.9%, 69%) hex: #ed8cb0

  

> color name lcol4 #44DBCA

Color 'lcol4' is opaque: rgb(26.7%, 85.9%, 79.2%) hex: #44dbca

  

> color name lcol5 #FF5F3B

Color 'lcol5' is opaque: rgb(100%, 37.3%, 23.1%) hex: #ff5f3b

  

> color name archcol1 #93B1E9

Color 'archcol1' is opaque: rgb(57.6%, 69.4%, 91.4%) hex: #93b1e9

  

> color name archcol2 #492376

Color 'archcol2' is opaque: rgb(28.6%, 13.7%, 46.3%) hex: #492376

  

> color name archcol3 #955B87

Color 'archcol3' is opaque: rgb(58.4%, 35.7%, 52.9%) hex: #955b87

  

> color name archcol4 #FEA398

Color 'archcol4' is opaque: rgb(99.6%, 63.9%, 59.6%) hex: #fea398

  

> color name archcol5 #C83320

Color 'archcol5' is opaque: rgb(78.4%, 20%, 12.5%) hex: #c83320

  

> color name archcol6 #FC9000

Color 'archcol6' is opaque: rgb(98.8%, 56.5%, 0%) hex: #fc9000

  

> color name archcol7 #FFD700

Color 'archcol7' is opaque: rgb(100%, 84.3%, 0%) hex: #ffd700

  

> color name crosscol1 #FAB06E

Color 'crosscol1' is opaque: rgb(98%, 69%, 43.1%) hex: #fab06e

  

> color name crosscol2 #E4766E

Color 'crosscol2' is opaque: rgb(89.4%, 46.3%, 43.1%) hex: #e4766e

  

> color name crosscol3 #E7723D

Color 'crosscol3' is opaque: rgb(90.6%, 44.7%, 23.9%) hex: #e7723d

  

> color name crosscol4 #99A87C

Color 'crosscol4' is opaque: rgb(60%, 65.9%, 48.6%) hex: #99a87c

  

> color name crosscol5 #6B968D

Color 'crosscol5' is opaque: rgb(42%, 58.8%, 55.3%) hex: #6b968d

  

> color name crosscol6 #73A2A9

Color 'crosscol6' is opaque: rgb(45.1%, 63.5%, 66.3%) hex: #73a2a9

  

> color name crosscol7 #005E75

Color 'crosscol7' is opaque: rgb(0%, 36.9%, 45.9%) hex: #005e75

  

> color name crosscol8 #0E2E61

Color 'crosscol8' is opaque: rgb(5.49%, 18%, 38%) hex: #0e2e61

  

> color name crosscol9 #D67FB0

Color 'crosscol9' is opaque: rgb(83.9%, 49.8%, 69%) hex: #d67fb0

  

> color name slidebg #f0f4ff

Color 'slidebg' is opaque: rgb(94.1%, 95.7%, 100%) hex: #f0f4ff

  

> color name egyptRed #E66735

Color 'egyptRed' is opaque: rgb(90.2%, 40.4%, 20.8%) hex: #e66735

  

> color name egyptBlue #008EB2

Color 'egyptBlue' is opaque: rgb(0%, 55.7%, 69.8%) hex: #008eb2

  

> color name egyptGreen #4FBD96

Color 'egyptGreen' is opaque: rgb(31%, 74.1%, 58.8%) hex: #4fbd96

  

> color name egyptYellow #FCBF67

Color 'egyptYellow' is opaque: rgb(98.8%, 74.9%, 40.4%) hex: #fcbf67

  
executed color.cxc  

> open function-keys.cxc

> functionkey F1 "ui mousemode right zoom"

> functionkey F2 "ui mousemode right 'translate selected models'"

> functionkey F7 "~cartoon; show; style stick"

> functionkey F8 "~show; cartoon"

> functionkey F12 "close"

executed function-keys.cxc  

> runscript open_separately.py

> alias iturn turn $1 $2 $3 models $4 center $4 $*

> alias openser open ~/Downloads/cryosparc_P$1_J$2_*_$3/*.mrc vser true

> alias vplay vser play $1 dir osc loop true startTime 1 cache 120

> alias vstop vser stop $1

> alias locres color sample $1 map $2 palette rdylbu key true range $3

> alias startserver remotecontrol rest start json true port 60312

executed init.cxc  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/rposert/Documents/talks/slac/chimerax-scripts/trpv1/consensus-
> refinement/J1295_map.mrc format mrc

Opened J1295_map.mrc as #1, grid size 256,256,256, pixel 1.22, shown at level
0.157, step 1, values float32  

> open 5irx

5irx title:  
Structure of TRPV1 in complex with DkTx and RTX, determined in lipid nanodisc
[more info...]  
  
Chain information for 5irx #2  
---  
Chain | Description | UniProt  
A B C D | Transient receptor potential cation channel subfamily V member 1 | TRPV1_RAT 110-603 627-764  
E F | Tau-theraphotoxin-Hs1a | DKTX_HAPSC 1-75  
  
Non-standard residues in 5irx #2  
---  
6EU — resiniferatoxin (RTX)  
6O8 —
(4R,7S)-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-7-[(pentanoyloxy)methyl]-3,5,8-trioxa-4lambda~5~-phosphatetradecan-1-aminium  
6O9 — (2S)-2-(acetyloxy)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}propyl
pentanoate  
6OE —
(2S)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexanoyloxy)propyl
hexanoate  
  

> color #1 near #2 far blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color zone #1 near #2 farColor blue

> hide #2 models

> show #2 models

> color zone #1 near #2 distance 10 farColor blue

> color zone #1 near #2 sharpEdges true farColor blue

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/color.py", line 1382, in color_zone  
color_zone(s, spoints, colors, distance, sharp_edges = sharp_edges,  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorzone.py", line 38, in color_zone  
zc.set_vertex_colors()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorzone.py", line 113, in set_vertex_colors  
color_zone_sharp_edges(surf, self.points, self.point_colors, self.distance,  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorzone.py", line 169, in color_zone_sharp_edges  
carray[:,:] = (surface.color if far_color is None or far_color == 'keep' else
far_color)  
^^^^^^^^^^^^^^^^^^^  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorzone.py", line 169, in color_zone_sharp_edges  
carray[:,:] = (surface.color if far_color is None or far_color == 'keep' else
far_color)  
^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> hide #2 models

> show #2 models

> volume #1 level 0.3899

> color zone #1 near #2 sharpEdges true farColor blue

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/color.py", line 1382, in color_zone  
color_zone(s, spoints, colors, distance, sharp_edges = sharp_edges,  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorzone.py", line 38, in color_zone  
zc.set_vertex_colors()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorzone.py", line 113, in set_vertex_colors  
color_zone_sharp_edges(surf, self.points, self.point_colors, self.distance,  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorzone.py", line 169, in color_zone_sharp_edges  
carray[:,:] = (surface.color if far_color is None or far_color == 'keep' else
far_color)  
^^^^^^^^^^^^^^^^^^^  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorzone.py", line 169, in color_zone_sharp_edges  
carray[:,:] = (surface.color if far_color is None or far_color == 'keep' else
far_color)  
^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> color zone #1 near #2 sharpEdges true farColor #0000FF

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/color.py", line 1382, in color_zone  
color_zone(s, spoints, colors, distance, sharp_edges = sharp_edges,  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorzone.py", line 38, in color_zone  
zc.set_vertex_colors()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorzone.py", line 113, in set_vertex_colors  
color_zone_sharp_edges(surf, self.points, self.point_colors, self.distance,  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorzone.py", line 169, in color_zone_sharp_edges  
carray[:,:] = (surface.color if far_color is None or far_color == 'keep' else
far_color)  
^^^^^^^^^^^^^^^^^^^  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorzone.py", line 169, in color_zone_sharp_edges  
carray[:,:] = (surface.color if far_color is None or far_color == 'keep' else
far_color)  
^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> color zone #1 near #2 sharpEdges true farColor keep

> color zone #1 near #2 sharpEdges true farColor #0000FF

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/color.py", line 1382, in color_zone  
color_zone(s, spoints, colors, distance, sharp_edges = sharp_edges,  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorzone.py", line 38, in color_zone  
zc.set_vertex_colors()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorzone.py", line 113, in set_vertex_colors  
color_zone_sharp_edges(surf, self.points, self.point_colors, self.distance,  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorzone.py", line 169, in color_zone_sharp_edges  
carray[:,:] = (surface.color if far_color is None or far_color == 'keep' else
far_color)  
^^^^^^^^^^^^^^^^^^^  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorzone.py", line 169, in color_zone_sharp_edges  
carray[:,:] = (surface.color if far_color is None or far_color == 'keep' else
far_color)  
^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> color zone #1 near #2 farColor #0000FF

> color zone #1 near #2 sharpEdges true

> close #1

> open /Users/rposert/Documents/talks/slac/chimerax-scripts/trpv1/consensus-
> refinement/J1294_map.mrc

Opened J1294_map.mrc as #1, grid size 256,256,256, pixel 1.22, shown at level
0.157, step 1, values float32  

> color zone #1 near #2 sharpEdges true farColor blue

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/color.py", line 1382, in color_zone  
color_zone(s, spoints, colors, distance, sharp_edges = sharp_edges,  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorzone.py", line 38, in color_zone  
zc.set_vertex_colors()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorzone.py", line 113, in set_vertex_colors  
color_zone_sharp_edges(surf, self.points, self.point_colors, self.distance,  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorzone.py", line 169, in color_zone_sharp_edges  
carray[:,:] = (surface.color if far_color is None or far_color == 'keep' else
far_color)  
^^^^^^^^^^^^^^^^^^^  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/colorzone.py", line 169, in color_zone_sharp_edges  
carray[:,:] = (surface.color if far_color is None or far_color == 'keep' else
far_color)  
^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac
      Model Identifier: Mac14,6
      Model Number: Z17500103LL/A
      Chip: Unknown
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 64 GB
      System Firmware Version: 10151.140.19
      OS Loader Version: 10151.140.19

Software:

    System Software Overview:

      System Version: macOS 14.6.1 (23G93)
      Kernel Version: Darwin 23.6.0
      Time since boot: 12 days, 4 hours, 52 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:
        DELL U2723QE:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 3840 x 2160 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.23.1
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    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: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    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: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    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: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    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: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    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-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    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: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11

[Eric Pettersen]

Reported by Rich Posert

[Tom Goddard]

Fixed in daily builds Sept 3, 2024 or newer.

The farColor option converted the color to a numpy array (r,g,b,a) and then compared that to the string "keep" which generates an error because of the way numpy does boolean comparison element-wise in arrays. I fixed the test to see if the far color is "keep" to first check if far color is a string.