Opened 3 years ago

Last modified 3 years ago

#8607 assigned defect

SEQCROW sticks preset sets key_light_color to 4 values instead of 3

Reported by: joegair@… Owned by: tony.schaefer@…
Priority: normal Milestone:
Component: General Controls Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
presets... sticks
command: lighting

Log:
> color name grey80 #333333

Color 'grey80' is opaque: gray(20%) hex: #333333

  

> color name grey65 #595959

Color 'grey65' is opaque: gray(34.9%) hex: #595959

  

> color name grey40 #999999

Color 'grey40' is opaque: gray(60%) hex: #999999

  

> color name grey20 #CCCCCC

Color 'grey20' is opaque: gray(80%) hex: #cccccc

  

> color name grey10 #E6E6E6

Color 'grey10' is opaque: gray(90.2%) hex: #e6e6e6

  

> color name grey3 #F7F7F7

Color 'grey3' is opaque: gray(96.9%) hex: #f7f7f7

  

> color name spartan #18453B

Color 'spartan' is opaque: rgb(9.41%, 27.1%, 23.1%) hex: #18453b

  

> color name msu_yellow #E6BF5C

Color 'msu_yellow' is opaque: rgb(90.2%, 74.9%, 36.1%) hex: #e6bf5c

  

> color name teal_light #49B0AB

Color 'teal_light' is opaque: rgb(28.6%, 69%, 67.1%) hex: #49b0ab

  

> color name teal_dark #1C7B81

Color 'teal_dark' is opaque: rgb(11%, 48.2%, 50.6%) hex: #1c7b81

  

> color name msu_blue #004583

Color 'msu_blue' is opaque: rgb(0%, 27.1%, 51.4%) hex: #004583

  

> color name excel #0B9A6D

Color 'excel' is opaque: rgb(4.31%, 60.4%, 42.7%) hex: #0b9a6d

  

> preset Ball-Stick-Endcap

Using preset: SEQCROW / Ball-Stick-Endcap  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/joe/Dropbox/Postdoc/calculations/organics/output/2R_3_pyridyl_pyrrolidine_eq_02_opt.out

Summary of feedback from opening
/Users/joe/Dropbox/Postdoc/calculations/organics/output/2R_3_pyridyl_pyrrolidine_eq_02_opt.out  
---  
note | 2R_3_pyridyl_pyrrolidine_eq_02_opt.out has 0 imaginary harmonic
vibrational modes  
  
Opened 2R_3_pyridyl_pyrrolidine_eq_02_opt.out as an ORCA output file  

> preset seqcrow ball-stick-endcap

Using preset: SEQCROW / Ball-Stick-Endcap  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> close session

> open
> /Users/joe/Dropbox/Postdoc/calculations/organics/output/2R_3_pyridyl_piperidine_eq_01_opt.out

Summary of feedback from opening
/Users/joe/Dropbox/Postdoc/calculations/organics/output/2R_3_pyridyl_piperidine_eq_01_opt.out  
---  
note | 2R_3_pyridyl_piperidine_eq_01_opt.out has 0 imaginary harmonic
vibrational modes  
  
Opened 2R_3_pyridyl_piperidine_eq_01_opt.out as an ORCA output file  

> close session

> open
> /Users/joe/Dropbox/Postdoc/calculations/organics/output/3R_3_pyridyl_piperidine_eq_02_opt.out

Summary of feedback from opening
/Users/joe/Dropbox/Postdoc/calculations/organics/output/3R_3_pyridyl_piperidine_eq_02_opt.out  
---  
note | 3R_3_pyridyl_piperidine_eq_02_opt.out has 0 imaginary harmonic
vibrational modes  
  
Opened 3R_3_pyridyl_piperidine_eq_02_opt.out as an ORCA output file  

> close session

> open
> /Users/joe/Dropbox/Postdoc/calculations/organics/output/3R_3_pyridyl_piperidine_eq_01_opt.out

Summary of feedback from opening
/Users/joe/Dropbox/Postdoc/calculations/organics/output/3R_3_pyridyl_piperidine_eq_01_opt.out  
---  
note | 3R_3_pyridyl_piperidine_eq_01_opt.out has 0 imaginary harmonic
vibrational modes  
  
Opened 3R_3_pyridyl_piperidine_eq_01_opt.out as an ORCA output file  

> open
> /Users/joe/Dropbox/Postdoc/calculations/organics/output/2R_3_pyridyl_pyrrolidine_eq_01_opt.out

Summary of feedback from opening
/Users/joe/Dropbox/Postdoc/calculations/organics/output/2R_3_pyridyl_pyrrolidine_eq_01_opt.out  
---  
note | 2R_3_pyridyl_pyrrolidine_eq_01_opt.out has 0 imaginary harmonic
vibrational modes  
  
Opened 2R_3_pyridyl_pyrrolidine_eq_01_opt.out as an ORCA output file  

> open
> /Users/joe/Dropbox/Postdoc/calculations/organics/output/2R_3_pyridyl_pyrrolidine_eq_02_opt.out

Summary of feedback from opening
/Users/joe/Dropbox/Postdoc/calculations/organics/output/2R_3_pyridyl_pyrrolidine_eq_02_opt.out  
---  
note | 2R_3_pyridyl_pyrrolidine_eq_02_opt.out has 0 imaginary harmonic
vibrational modes  
  
Opened 2R_3_pyridyl_pyrrolidine_eq_02_opt.out as an ORCA output file  

> close #3

> preset seqcrow ball-stick-endcap

Using preset: SEQCROW / Ball-Stick-Endcap  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> hide H

> ui mousemode right translate

> ui mousemode right "translate selected models"

> select add #1

26 atoms, 27 bonds, 1 residue, 1 model selected  

> view matrix models #1,1,0,0,-0.25648,0,1,0,-2.4108,0,0,1,-0.043008

> ui mousemode right translate

> select subtract #1

Nothing selected  

> color N msu_blue

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

> color #*/a N msu_blue

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

> color #*/a&N msu_blue

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

> select all

49 atoms, 51 bonds, 2 residues, 2 models selected  

> color N red

> color N msu_blue

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

> color sel msu_blue

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

> ui mousemode right "translate selected models"

> view matrix models #1,1,0,0,-0.21399,0,1,0,-3.0451,0,0,1,1.309

> color N msu_blue

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

> color name msu_blue #004583

Color 'msu_blue' is opaque: rgb(0%, 27.1%, 51.4%) hex: #004583

  

> select subtract #1

Nothing selected  

> ui mousemode right select

> select #1/a:1@N1

1 atom, 1 residue, 1 model selected  

> color sel msu_blue

> select #1/a:1@N1

1 atom, 1 residue, 1 model selected  

> select clear

> color N msu_blue

> color C grey40

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

> select #2/a:1@C1

1 atom, 1 residue, 1 model selected  

> color sel grey40

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

> color name grey40 #999999

Color 'grey40' is opaque: gray(60%) hex: #999999

  

> color C grey40

[Repeated 1 time(s)]

> color C grey

> color C grey40

> color name excel #0B9A6D

Color 'excel' is opaque: rgb(4.31%, 60.4%, 42.7%) hex: #0b9a6d

  

> color #1&C excel

> select #2/a:1@C1

1 atom, 1 residue, 1 model selected  

> select #2/a:1@C1

1 atom, 1 residue, 1 model selected  

> select #2/a:1@C1

1 atom, 1 residue, 1 model selected  

> select #2/a:1@C1

1 atom, 1 residue, 1 model selected  

> select #2/a:1@N2

1 atom, 1 residue, 1 model selected  

> select add #2/a:1@C6

2 atoms, 1 residue, 1 model selected  

> select add #2/a:1@C7

3 atoms, 1 residue, 1 model selected  

> select add #2/a:1@C8

4 atoms, 1 residue, 1 model selected  

> select subtract #2/a:1@C6

3 atoms, 1 residue, 1 model selected  

> select subtract #2/a:1@C7

2 atoms, 1 residue, 1 model selected  

> select subtract #2/a:1@C8

1 atom, 1 residue, 1 model selected  

> select subtract #2/a:1@N2

Nothing selected  

> select add #2/a:1@N1

1 atom, 1 residue, 1 model selected  

> select add #2/a:1@C5

2 atoms, 1 residue, 1 model selected  

> select add #2/a:1@C4

3 atoms, 1 residue, 1 model selected  

> select add #2/a:1@C3

4 atoms, 1 residue, 1 model selected  

> select add #2/a:1@C1

5 atoms, 1 residue, 1 model selected  

> select add #2/a:1@C2

6 atoms, 1 residue, 1 model selected  

> select #2/a:1@C6

1 atom, 1 residue, 1 model selected  

> select #2/a:1@C6

1 atom, 1 residue, 1 model selected  

> select #1/a:1@N1

1 atom, 1 residue, 1 model selected  

> select #1/a:1@C9

1 atom, 1 residue, 1 model selected  

> select #1/a:1@C8

1 atom, 1 residue, 1 model selected  

> select #1/a:1@N1

1 atom, 1 residue, 1 model selected  

> align #1/a:1@O4,C2,C3,C4,C5 toAtoms #2/a:1@N1,C5,

Invalid "toAtoms" argument: only initial part "#2/a:1@N1,C5" of atom specifier
valid  

> align #1/a:1@N1, C9,C8, toAtoms #2/a:1@N1,C5,C4,C3,C1, C2,C6

Missing required "to_atoms" argument  

> view

> select #1/a:1@N1

1 atom, 1 residue, 1 model selected  

> select add #1

26 atoms, 27 bonds, 1 residue, 1 model selected  

> select subtract #1

Nothing selected  

> align #1/a:1@N1, C9,C8,C7,C5,C6,C2 toAtoms #2/a:1@N1,C5,C4,C3,C1, C2,C6

RMSD between 7 atom pairs is 0.014 angstroms  

> preset seqcrow sticks

Using preset: SEQCROW / Sticks  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset seqcrow "ball-stick-endcap 2"

Using preset: SEQCROW / Ball-Stick-Endcap 2  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset seqcrow "sticks 2"

Using preset: SEQCROW / Sticks 2  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #1/a:1@N1, C9,C8,C7,C5,C6,C2

> hide #1/a:1@N1, C9,C8,C7,C5,C6

> hide #1 models

> show #1 models

> hide #2 models

> show #2 models

> color #1 grey40

> color #2 grey40

> color #1 excel

> color N msu_blue

> set bgColor white

> lighting soft

> undo

[Repeated 1 time(s)]

> preset seqcrow sticks

Using preset: SEQCROW / Sticks  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> color #2 grey40

> color #1 excel

> color N msu_blue

> size #1&2 stickRadius 0.15

Expected a keyword  

> size #1 stickRadius 0.15

Changed 27 bond radii  

> size stickRadius 0.15

Changed 51 bond radii  

> size stickRadius 0.18

Changed 51 bond radii  

> preset seqcrow "ball-stick-endcap 2"

Using preset: SEQCROW / Ball-Stick-Endcap 2  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset seqcrow sticks

Using preset: SEQCROW / Sticks  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset seqcrow "sticks 2"

Using preset: SEQCROW / Sticks 2  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> size stickRadius 0.18

Changed 51 bond radii  

> size stickRadius 0.2

Changed 51 bond radii  

> size stickRadius 0.18

Changed 51 bond radii  

> color #1 grey40

> color#2 excel

Unknown command: color#2 excel  

> color #2 excel

> color #1 excel

> color #2 grey40

> select #2/a:1@C1

1 atom, 1 residue, 1 model selected  

> select #2/a:1@C1

1 atom, 1 residue, 1 model selected  

> color #2 msu_yellow

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

> color #2 spartan

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

> color name spartan #18453B

Color 'spartan' is opaque: rgb(9.41%, 27.1%, 23.1%) hex: #18453b

  

> color #2 spartan

> select add #2/a:1@C3

2 atoms, 1 residue, 1 model selected  

> select add #2/a:1@C4

3 atoms, 1 residue, 1 model selected  

> select add #2/a:1@C5

4 atoms, 1 residue, 1 model selected  

> select add #2/a:1@N1

5 atoms, 1 residue, 1 model selected  

> select add #2/a:1@C2

6 atoms, 1 residue, 1 model selected  

> color sel grey40

> color N msu_blue

> view

> select add #2

23 atoms, 24 bonds, 1 residue, 1 model selected  

> select subtract #2

Nothing selected  

> select clear

> ui mousemode right clip

[Repeated 1 time(s)]

> lighting full

> lighting soft

> lighting flat

> lighting shadows true intensity 0.5

> graphics silhouettes false

> lighting shadows false

> lighting flat

> lighting full

> lighting soft

> lighting simple

> color name msu_yellow #E6BF5C

Color 'msu_yellow' is opaque: rgb(90.2%, 74.9%, 36.1%) hex: #e6bf5c

  

> view

> size stickRadius 0.17

Changed 51 bond radii  

> color #1 msu_yellow

> color #2 msu_yellow

> color #1 excel

> undo

> color #1 excel

> ui mousemode right select

Drag select of 6 atoms, 6 bonds  

> color sel grey40

> select clear

> color N msu_blue

> color name teal_light #49B0AB

Color 'teal_light' is opaque: rgb(28.6%, 69%, 67.1%) hex: #49b0ab

  

> color name teal_dark #1C7B81

Color 'teal_dark' is opaque: rgb(11%, 48.2%, 50.6%) hex: #1c7b81

  

> color #2 teal_light

> color N msu_blue

> color #2 teal_dark

Drag select of 6 atoms, 6 bonds  

> color sel grey40

> color N msu_blue

> select add #2

23 atoms, 24 bonds, 1 residue, 1 model selected  

> select clear

[Repeated 1 time(s)]

> lighting

Intensity: 1  
Direction: 0.577,-0.577,-0.577  
Color: 100,100,100  
Fill intensity: 0.5  
Fill direction: -0.2,-0.2,-0.959  
Fill color: 100,100,100  
Ambient intensity: 0.4  
Ambient color: 100,100,100  
Depth cue: 1, start 0.5, end 1, color 100,100,100  
Shadow: False (depth map size 2048, depth bias 0.005)  
Multishadows: 0 (max 1024, depth map size 1024, depth bias 0.01)  

> fill intensity .2

Unknown command: fill intensity .2  

> lighting fill intensity 0.2

Expected keyword "fillColor", "fillDirection", or "fillIntensity"  

> lighting fillIntensity 0.2

> lighting fillIntensity 0.3

> lighting intensity 0.3

> lighting intensity 0.5

> lighting intensity 0.8

> lighting fillIntensity 0.8

> lighting fillIntensity 0.5

> lighting ambientIntensity 0.5

> lighting ambientIntensity 0.1

> lighting ambientIntensity 0.2

> lighting ambientIntensity 0.3

> lighting simple

> lighting soft

> lighting full

> lighting soft

> lighting shadows true intensity 0.5

> lighting flat

> lighting full

> lighting soft

> lighting simple

> lighting soft

> lighting gentle

> lighting depthCue false

> preset seqcrow sticks

Using preset: SEQCROW / Sticks  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> lighting

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/lighting.py", line 100, in lighting  
'Color: %d,%d,%d' % tuple(100*r for r in lp.key_light_color),  
TypeError: not all arguments converted during string formatting  
  
TypeError: not all arguments converted during string formatting  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/lighting.py", line 100, in lighting  
'Color: %d,%d,%d' % tuple(100*r for r in lp.key_light_color),  
  
See log for complete Python traceback.  
  

> lighting

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/lighting.py", line 100, in lighting  
'Color: %d,%d,%d' % tuple(100*r for r in lp.key_light_color),  
TypeError: not all arguments converted during string formatting  
  
TypeError: not all arguments converted during string formatting  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/lighting.py", line 100, in lighting  
'Color: %d,%d,%d' % tuple(100*r for r in lp.key_light_color),  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
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: MacBookPro16,1
      Processor Name: 6-Core Intel Core i7
      Processor Speed: 2.6 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 12 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 1731.140.2.0.0 (iBridge: 19.16.16064.0.0,0)
      OS Loader Version: 540.120.3~19

Software:

    System Software Overview:

      System Version: macOS 12.5 (21G72)
      Kernel Version: Darwin 21.6.0
      Time since boot: 24 days 13:08

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0000
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2

    AMD Radeon Pro 5300M:

      Chipset Model: AMD Radeon Pro 5300M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0043
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32207P1-019
      Option ROM Version: 113-D32207P1-019
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    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-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    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: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    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: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    Send2Trash: 1.8.0
    SEQCROW: 1.5.14
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0

Change History (4)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → General Controls
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Lighting: not all arguments converted during string formatting

Reported by Joe Gair

comment:2 by Tom Goddard, 3 years ago

Owner: changed from Tom Goddard to tony.schaefer@…
Summary: Lighting: not all arguments converted during string formatting → SEQCROW sticks preset sets key_light_color to 4 values instead of 3

This is a bug in the SEQCROW package in command "preset seqcrow sticks". It set the lighting key_light_color to [1,1,1,0] four values, but the color is supposed to 3 values (red,green,blue).

Here is the ChimeraX programming documentation about the Lighting class

https://www.rbvi.ucsf.edu/chimerax/docs/devel/modules/graphics/graphics.html#chimerax.graphics.opengl.Lighting

Tony Schaefer the SEQCROW developer will have to fix this. If you avoid "preset seqcrow sticks" you will not get this error..

in reply to:  3 ; comment:3 by tony.schaefer@…, 3 years ago 

Joe,

This should be fixed in SEQCROW 1.6.1, which is now on the toolshed (Tools -> More Tools... on the ChimeraX menu). SEQCROW presets are "secretly" applied in a lot of situations, like editing structures using one of SEQCROW's tools. I did that because the default atom style is not conducive to editing. This makes the preset difficult to avoid. Sorry for the inconvenience.

Tom, in the future please forward SEQCROW-related bugs to my new gmail (tony.schaefer.chem ...). My UGA email expires in a few months.

Best,

Tony
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Tuesday, March 7, 2023 5:53 PM
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; joegair@msu.edu <joegair@msu.edu>; Anthony James Schaefer <tony.schaefer@uga.edu>
Subject: Re: [ChimeraX] #8607: SEQCROW sticks preset sets key_light_color to 4 values instead of 3 (was: Lighting: not all arguments converted during string formatting)

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]


#8607: SEQCROW sticks preset sets key_light_color to 4 values instead of 3
---------------------------------------+-----------------------------
          Reporter:  joegair@…         |      Owner:  tony.schaefer@…
              Type:  defect            |     Status:  assigned
          Priority:  normal            |  Milestone:
         Component:  General Controls  |    Version:
        Resolution:                    |   Keywords:
        Blocked By:                    |   Blocking:
Notify when closed:                    |   Platform:  all
           Project:  ChimeraX          |
---------------------------------------+-----------------------------
Changes (by Tom Goddard):

 * owner:  Tom Goddard => tony.schaefer@…


Comment:

 This is a bug in the SEQCROW package in command "preset seqcrow sticks".
 It set the lighting key_light_color to [1,1,1,0] four values, but the
 color is supposed to 3 values (red,green,blue).

 Here is the ChimeraX programming documentation about the Lighting class

 https://www.rbvi.ucsf.edu/chimerax/docs/devel/modules/graphics/graphics.html#chimerax.graphics.opengl.Lighting

 Tony Schaefer the SEQCROW developer will have to fix this.  If you avoid
 "preset seqcrow sticks" you will not get this error..

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/8607#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

in reply to:  4 ; comment:4 by goddard@…, 3 years ago 

I will use your new email.  I saw both and wasn't sure which one to use.  It is fine to change styles secretly if it suits your need.  With the ChimeraX bug reporting on any traceback you will get pretty quick feedback if there is any change that breaks common SEQCROW uses.  This problem must not have triggered errors and the 4th color component was perhaps silently ignored by most code.
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