Color/depth changes based on lighting

[coyote_v2002@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
I superposed several nearly identical receptors to highlight different position of one sidechain. Probably itcould be done more efficiently,  but that's not why I am reporting this.  Here's the bug: the color of the protein changes if we sswitch from simple to soft or full lighting. In other words, with different lighting other models emerge as foreground.

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open
> /Users/visvaldas/Documents/work/quinone_reductase/green_3nitro_PNDPO_fig.cxs
> format session

Log from Wed Feb 9 05:54:01 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open
> /Users/visvaldas/Documents/work/quinone_reductase/green_3nitro_PNDPO_fig.cxs
> format session

Log from Tue Feb 8 22:40:34 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open
> /Users/visvaldas/Documents/work/quinone_reductase/green_3nitro_PNDPO_fig.cxs
> format session

Log from Tue Feb 8 18:19:29 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open
> /Users/visvaldas/Documents/work/quinone_reductase/green_red_3nitro_fig.cxs
> format session

Log from Tue Feb 8 17:22:02 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1qrd2_ref.pdbqt

Chain information for 1qrd2_ref.pdb #1  
---  
Chain | Description  
A B | No description available  
  
Opened 1qrd2_ref.pdbqt containing 1 structures (5369 atoms, 5488 bonds)  

> open 1qrd2Y128/green_4/FADOx_receptor.pdbqt

Chain information for FADOx_receptor.pdb #2  
---  
Chain | Description  
A B | No description available  
  
Opened FADOx_receptor.pdbqt containing 1 structures (5369 atoms, 5488 bonds)  

> open 1qrd2/FADOx_receptor.pdbqt

Chain information for FADOx_receptor.pdb #3  
---  
Chain | Description  
A B | No description available  
  
Opened FADOx_receptor.pdbqt containing 1 structures (5369 atoms, 5488 bonds)  

> open 1qrd2Y128/green_4/3nitroNPDO_ox_docked_1.pdbqt

Summary of feedback from opening
1qrd2Y128/green_4/3nitroNPDO_ox_docked_1.pdbqt  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK minimizedAffinity -8.39384747  
  
Ignored bad PDB record found on line 2  
REMARK minimizedRMSD -1  
  
Ignored bad PDB record found on line 3  
REMARK 1 active torsions:  
  
Ignored bad PDB record found on line 4  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
Ignored bad PDB record found on line 5  
REMARK 1 A between atoms: C5_5 and N3_20  
  
5 messages similar to the above omitted  
  
Opened 3nitroNPDO_ox_docked_1.pdbqt containing 1 structures (22 atoms, 25
bonds)  

> open 1qrd2Y128/green_4/3nitroPNPDO_ox_docked_1.pdbqt

Summary of feedback from opening
1qrd2Y128/green_4/3nitroPNPDO_ox_docked_1.pdbqt  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK minimizedAffinity -8.26599312  
  
Ignored bad PDB record found on line 2  
REMARK minimizedRMSD -1  
  
Ignored bad PDB record found on line 3  
REMARK 1 active torsions:  
  
Ignored bad PDB record found on line 4  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
Ignored bad PDB record found on line 5  
REMARK 1 A between atoms: C6_6 and N4_20  
  
5 messages similar to the above omitted  
  
Opened 3nitroPNPDO_ox_docked_1.pdbqt containing 1 structures (22 atoms, 25
bonds)  

> open 1qrd2Y128/green_4/NPDO_ox_docked_1.pdbqt

Summary of feedback from opening 1qrd2Y128/green_4/NPDO_ox_docked_1.pdbqt  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK minimizedAffinity -7.901546  
  
Ignored bad PDB record found on line 2  
REMARK minimizedRMSD -1  
  
Ignored bad PDB record found on line 3  
REMARK 0 active torsions:  
  
Ignored bad PDB record found on line 4  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
Ignored bad PDB record found on line 5  
ROOT  
  
2 messages similar to the above omitted  
  
Opened NPDO_ox_docked_1.pdbqt containing 1 structures (19 atoms, 22 bonds)  

> open 1qrd2Y128/green_4/PNDPO_ox_docked_1.pdbqt

Summary of feedback from opening 1qrd2Y128/green_4/PNDPO_ox_docked_1.pdbqt  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK minimizedAffinity -7.76308203  
  
Ignored bad PDB record found on line 2  
REMARK minimizedRMSD -1  
  
Ignored bad PDB record found on line 3  
REMARK 0 active torsions:  
  
Ignored bad PDB record found on line 4  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
Ignored bad PDB record found on line 5  
ROOT  
  
2 messages similar to the above omitted  
  
Opened PNDPO_ox_docked_1.pdbqt containing 1 structures (19 atoms, 22 bonds)  

> open 1qrd2/3nitroNPDO_ox_docked_1.pdbqt

Summary of feedback from opening 1qrd2/3nitroNPDO_ox_docked_1.pdbqt  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK minimizedAffinity -8.51486588  
  
Ignored bad PDB record found on line 2  
REMARK minimizedRMSD -1  
  
Ignored bad PDB record found on line 3  
REMARK 1 active torsions:  
  
Ignored bad PDB record found on line 4  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
Ignored bad PDB record found on line 5  
REMARK 1 A between atoms: C5_5 and N3_20  
  
5 messages similar to the above omitted  
  
Opened 3nitroNPDO_ox_docked_1.pdbqt containing 1 structures (22 atoms, 25
bonds)  

> open 1qrd2/3nitroPNPDO_ox_docked_1.pdbqt

Summary of feedback from opening 1qrd2/3nitroPNPDO_ox_docked_1.pdbqt  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK minimizedAffinity -8.27984142  
  
Ignored bad PDB record found on line 2  
REMARK minimizedRMSD -1  
  
Ignored bad PDB record found on line 3  
REMARK 1 active torsions:  
  
Ignored bad PDB record found on line 4  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
Ignored bad PDB record found on line 5  
REMARK 1 A between atoms: C6_6 and N4_20  
  
5 messages similar to the above omitted  
  
Opened 3nitroPNPDO_ox_docked_1.pdbqt containing 1 structures (22 atoms, 25
bonds)  

> open 1qrd2/NPDO_ox_docked_1.pdbqt

Summary of feedback from opening 1qrd2/NPDO_ox_docked_1.pdbqt  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK minimizedAffinity -8.0473671  
  
Ignored bad PDB record found on line 2  
REMARK minimizedRMSD -1  
  
Ignored bad PDB record found on line 3  
REMARK 0 active torsions:  
  
Ignored bad PDB record found on line 4  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
Ignored bad PDB record found on line 5  
ROOT  
  
2 messages similar to the above omitted  
  
Opened NPDO_ox_docked_1.pdbqt containing 1 structures (19 atoms, 22 bonds)  

> open 1qrd2/PNDPO_ox_docked_1.pdbqt

Summary of feedback from opening 1qrd2/PNDPO_ox_docked_1.pdbqt  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK minimizedAffinity -7.86091995  
  
Ignored bad PDB record found on line 2  
REMARK minimizedRMSD -1  
  
Ignored bad PDB record found on line 3  
REMARK 0 active torsions:  
  
Ignored bad PDB record found on line 4  
REMARK status: ('A' for Active; 'I' for Inactive)  
  
Ignored bad PDB record found on line 5  
ROOT  
  
2 messages similar to the above omitted  
  
Opened PNDPO_ox_docked_1.pdbqt containing 1 structures (19 atoms, 22 bonds)  

> save
> /Users/visvaldas/Documents/work/quinone_reductase/green_red_3nitro_fig.cxs

> hide #1 models

> hide #3 models

> hide #4 models

> hide #5 models

> hide #6 models

> hide #7 models

> hide #8 models

> hide #9 models

> hide #10 models

> hide #11 models

> select #2:128

28 atoms, 28 bonds, 2 residues, 1 model selected  

> select #2/A:128

14 atoms, 14 bonds, 1 residue, 1 model selected  

> show sel target ab

> select clear

> show #3 models

> hide #2 models

> select #3/A:128

14 atoms, 14 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> select H

2853 atoms, 1557 residues, 3 models selected  

> delete atoms (#3 & sel)

> delete bonds (#3 & sel)

> select B

6 atoms, 3 residues, 3 models selected  

> delete atoms (#3 & sel)

> delete bonds (#3 & sel)

> select clear

> save
> /Users/visvaldas/Documents/work/quinone_reductase/green_red_3nitro_fig.cxs

> show #2 models

> show #1 models

> select ::name="FAD"

176 atoms, 191 bonds, 3 residues, 3 models selected  

> color sel purple

> color sel byhetero

> save
> /Users/visvaldas/Documents/work/quinone_reductase/green_red_3nitro_fig.cxs

> select clear

> hide #3 models

> hide #2 models

> hide #1 models

> show #1 models

> show #2 models

> show #3 models

> show #4 models

> show #11 models

> show #10 models

> show #9 models

> show #5 models

> show #6 models

> show #7 models

> show #8 models

> select H

1902 atoms, 1038 residues, 2 models selected  

> delete atoms sel

> delete bonds sel

> select clear

> save
> /Users/visvaldas/Documents/work/quinone_reductase/green_red_3nitro_fig.cxs

[Repeated 1 time(s)]

> select #2/A:128@CD1

1 atom, 1 residue, 1 model selected  

> select up

12 atoms, 12 bonds, 1 residue, 1 model selected  

> color sel lime

> select #3/A:128@CD2

1 atom, 1 residue, 1 model selected  

> select up

12 atoms, 12 bonds, 1 residue, 1 model selected  

> color sel red

> save
> /Users/visvaldas/Documents/work/quinone_reductase/green_red_3nitro_fig.cxs

——— End of log from Tue Feb 8 17:22:02 2022 ———

opened ChimeraX session  

> select clear

> hide #3 models

> hide #9 models

> hide #8 models

> hide #7 models

> hide #6 models

> show #6 models

> hide #10 models

> hide #11 models

> select #1/A:127

7 atoms, 6 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> select #1/A:126

12 atoms, 12 bonds, 1 residue, 1 model selected  

> show sel atoms

> show #7 models

> save
> /Users/visvaldas/Documents/work/quinone_reductase/green_3nitro_PNDPO_fig.cxs

——— End of log from Tue Feb 8 18:19:29 2022 ———

opened ChimeraX session  

> hide #6 models

> hide #4 models

> select #5/?:1@O3

1 atom, 1 residue, 1 model selected  

> select add #1/A:127@OG1

2 atoms, 2 residues, 2 models selected  

> ui tool show Distances

> distance style symbol false

> distance #5/?:1@O3 #1/A:127@OG1

Distance between 3nitroPNPDO_ox_docked_1.pdb #5/? UNK 1 O3 and 1qrd2_ref.pdb
#1/A THR 127 OG1: 2.621  

> hide #12.1 models

> distance style color #aa7942

> distance style color black

[Repeated 2 time(s)]

> distance style color #010101

> distance style color #040404

> distance style color #0a0a0a

> distance style color #101010

> distance style color #202020

> distance style color #282828

> distance style color #313131

> distance style color #434343

> distance style color #4e4e4e

> distance style color #5b5b5b

> distance style color #676767

> distance style color #7b7b7b

> distance style color #858585

> distance style color #8d8d8d

> distance style color #949494

> distance style color #a0a0a0

> distance style color #a4a4a4

> distance style color #a8a8a8

> distance style color #aeaeae

> distance style color #b1b1b1

> distance style color #b4b4b4

> distance style color #b9b9b9

> distance style color #bbbbbb

> distance style color #bdbdbd

> distance style color silver

> distance style color #c3c3c3

[Repeated 4 time(s)]

> distance style color #c2c2c2

[Repeated 3 time(s)]

> distance style color #c1c1c1

[Repeated 1 time(s)]

> distance style color #bfbfbf

[Repeated 1 time(s)]

> distance style color #bebebe

[Repeated 1 time(s)]

> distance style color #bdbdbd

> distance style color #b8b8b8

> distance style color #b5b5b5

> distance style color #b1b1b1

> distance style color #aaaaaa

> distance style color #a6a6a6

> distance style color #a3a3a3

> distance style color #a0a0a0

> distance style color #9e9e9e

> distance style color #9c9c9c

> distance style color #9b9b9b

> distance style color #9a9a9a

> distance style color #989898

> distance style color #969696

> distance style color #949494

> distance style color #939393

> distance style color #919191

[Repeated 1 time(s)]

> distance style color #909090

[Repeated 1 time(s)]

> distance style color #8f8f8f

[Repeated 2 time(s)]

> distance style color #8e8e8e

[Repeated 2 time(s)]

> distance style color #8d8d8d

[Repeated 1 time(s)]

> distance style color #8c8c8c

> distance style color #8a8a8a

> distance style color #898989

[Repeated 1 time(s)]

> distance style color #888888

[Repeated 1 time(s)]

> distance style color #878787

> distance style color #858585

[Repeated 1 time(s)]

> distance style color #848484

[Repeated 2 time(s)]

> distance style color #838383

[Repeated 3 time(s)]

> distance style color #828282

> distance style color #818181

> distance style color grey

[Repeated 1 time(s)]

> save
> /Users/visvaldas/Documents/work/quinone_reductase/green_3nitro_PNDPO_fig.cxs

> select clear

> hide #7 models

> select #5/?:1@N1

1 atom, 1 residue, 1 model selected  

> select add #1/A:126@OH

2 atoms, 2 residues, 2 models selected  

> distance #5/?:1@N1 #1/A:126@OH

Distance between 3nitroPNPDO_ox_docked_1.pdb #5/? UNK 1 N1 and 1qrd2_ref.pdb
#1/A TYR 126 OH: 3.115  

> select clear

> log metadata #1-11

No models had metadata

> log chains #1-11

Chain information for 1qrd2_ref.pdb #1  
---  
Chain | Description  
A B | No description available  
  
Chain information for FADOx_receptor.pdb #2  
---  
Chain | Description  
A B | No description available  
  
Chain information for FADOx_receptor.pdb #3  
---  
Chain | Description  
A B | No description available  
  

> distance style color grey

> select #5/?:1@N3

1 atom, 1 residue, 1 model selected  

> select add #1/A:126@OH

2 atoms, 2 residues, 2 models selected  

> distance #5/?:1@N3 #1/A:126@OH

Distance between 3nitroPNPDO_ox_docked_1.pdb #5/? UNK 1 N3 and 1qrd2_ref.pdb
#1/A TYR 126 OH: 2.903  

> distance style color grey

> save
> /Users/visvaldas/Documents/work/quinone_reductase/green_3nitro_PNDPO_fig.cxs

[Repeated 1 time(s)]

——— End of log from Tue Feb 8 22:40:34 2022 ———

opened ChimeraX session  

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> select clear

> ui tool show "Side View"

> save
> /Users/visvaldas/Documents/work/quinone_reductase/green_3nitro_PNDPO_fig.cxs

No visible atoms, bonds, or surfaces selected  

> color #12 #fffb00 models transparency 0

> select clear

> show #7 models

> hide #7 models

> save
> /Users/visvaldas/Documents/work/quinone_reductase/green_3nitro_PNDPO_fig.cxs

——— End of log from Wed Feb 9 05:54:01 2022 ———

opened ChimeraX session  

> save
> /Users/visvaldas/Documents/work/quinone_reductase/green_red_3nitro_fig.cxs

> save
> /Users/visvaldas/Documents/work/quinone_reductase/green_3nitro_PNDPO_fig.cxs

> select :105

84 atoms, 90 bonds, 6 residues, 3 models selected  

> hide sel & #1-2 atoms

> select clear

> select :1-104

5156 atoms, 5282 bonds, 632 residues, 11 models selected  

> select :3-104

4920 atoms, 5022 bonds, 612 residues, 3 models selected  

> hide sel & #1-2 atoms

> select :127-300

7174 atoms, 7369 bonds, 885 residues, 3 models selected  

> select :129-300

7060 atoms, 7249 bonds, 873 residues, 3 models selected  

> hide sel & #1-2 atoms

> undo

> select :129-250

5844 atoms, 5994 bonds, 732 residues, 3 models selected  

> hide sel & #1-2 atoms

> select :106

66 atoms, 66 bonds, 6 residues, 3 models selected  

> hide sel & #1-2 atoms

> select clear

> save
> /Users/visvaldas/Documents/work/quinone_reductase/green_3nitro_PNDPO_fig.cxs

> lighting full

> lighting simple

> lighting soft

> lighting full

> lighting simple

> save
> /Users/visvaldas/Documents/work/quinone_reductase/green_3nitro_PNDPO_fig.cxs

> save /Users/visvaldas/Documents/work/quinone_reductase/test.cxs

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> lighting full

> lighting soft

> lighting simple

> hide #2 models

> show #2 models




OpenGL version: 4.1 INTEL-18.4.6
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,3
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 1.4 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 1715.81.2.0.0 (iBridge: 19.16.10744.0.0,0)
      OS Loader Version: 540.80.2~11

Software:

    System Software Overview:

      System Version: macOS 12.2 (21D49)
      Kernel Version: Darwin 21.3.0
      Time since boot: 13 days 8:15

Graphics/Displays:

    Intel Iris Plus Graphics 645:

      Chipset Model: Intel Iris Plus Graphics 645
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea6
      Revision ID: 0x0001
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    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
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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
    suds-jurko: 0.6
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
File attachment: test.cxs

test.cxs​

[coyote_v2002@…]

Added by email2trac

[pett]

Reported by Visvaldas Kairys

[Tom Goddard]

You have a brown and blue ribbon that are identical both shown. The brown shows for simple lighting and the blue for soft and full lighting.

Unfortunately ChimeraX does not guarantee which model is shown when two identical models are on top of each other -- with some graphics drivers it may even show a mottled mix of both. The rendering pipeline uses multiple passes and the shadowing of the soft and full lighting mode change the order.

This is not something we are going to fix -- too hard for too rare a use. It would make sense for you to make a single model showing the residue 128 rotamer you want instead of trying to combine two nearly identical models on top of each other. If you don't want to do that then you can hack things by renumber the model numbers, for example command "rename #1 id #15" reverses the ordering of brown (#1) and blue (#2) models and reverses which one appears on top.