Selection highlighting not continuous

[hwang@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
When I select residues, the display of green highlighting is not continuous.

Log:
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/hwang/Dropbox/Mac/Documents/Manu/TMEM208_Consurf/AF_Q9BTX3_F1_model_v2_1__pdb_ATOMS_section_With_ConSurf.pdb

AF_Q9BTX3_F1_model_v2_1__pdb_ATOMS_section_With_ConSurf.pdb title:  
Alphafold monomer V2.0 prediction for transmembrane protein 208 (Q9BTX3) [more
info...]  
  
Chain information for
AF_Q9BTX3_F1_model_v2_1__pdb_ATOMS_section_With_ConSurf.pdb #1  
---  
Chain | Description | UniProt  
A | transmembrane protein 208 | TM208_HUMAN  
  

> select /A:72

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /A:73

6 atoms, 5 bonds, 1 residue, 1 model selected  

> view clip false

> view sel

> view clip false

> color bfactor sel

6 atoms, 1 residues, atom bfactor range 6 to 6  

> select add #1

1384 atoms, 1420 bonds, 173 residues, 1 model selected  

> color bfactor sel

1384 atoms, 173 residues, atom bfactor range 1 to 9  

> ui tool show "Side View"

> ui windowfill toggle

> select up

1384 atoms, 1420 bonds, 173 residues, 1 model selected  

> select up

1384 atoms, 1420 bonds, 173 residues, 1 model selected  

> select up

1384 atoms, 1420 bonds, 173 residues, 1 model selected  

> ui windowfill toggle

> view sel

[Repeated 1 time(s)]

> ui windowfill toggle

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for
AF_Q9BTX3_F1_model_v2_1__pdb_ATOMS_section_With_ConSurf.pdb_A SES surface
#1.1: minimum, -12.30, mean 0.80, maximum 19.19  
To also show corresponding color key, enter the above coulombic command and
add key true  

> open
> /Volumes/hwang/alphaFold/TMEM208/di/TMEM208_di_fee2e_unrelaxed_rank_5_model_5.pdb
> /Volumes/hwang/alphaFold/TMEM208/di/TMEM208_di_fee2e_unrelaxed_rank_4_model_2.pdb
> /Volumes/hwang/alphaFold/TMEM208/di/TMEM208_di_fee2e_unrelaxed_rank_3_model_1.pdb
> /Volumes/hwang/alphaFold/TMEM208/di/TMEM208_di_fee2e_unrelaxed_rank_2_model_3.pdb
> /Volumes/hwang/alphaFold/TMEM208/di/TMEM208_di_fee2e_unrelaxed_rank_1_model_4.pdb

Chain information for TMEM208_di_fee2e_unrelaxed_rank_5_model_5.pdb #2  
---  
Chain | Description  
B | No description available  
C | No description available  
  
Chain information for TMEM208_di_fee2e_unrelaxed_rank_4_model_2.pdb #3  
---  
Chain | Description  
B | No description available  
C | No description available  
  
Chain information for TMEM208_di_fee2e_unrelaxed_rank_3_model_1.pdb #4  
---  
Chain | Description  
B | No description available  
C | No description available  
  
Chain information for TMEM208_di_fee2e_unrelaxed_rank_2_model_3.pdb #5  
---  
Chain | Description  
B | No description available  
C | No description available  
  
Chain information for TMEM208_di_fee2e_unrelaxed_rank_1_model_4.pdb #6  
---  
Chain | Description  
B | No description available  
C | No description available  
  

> tile

6 models tiled  

> ui windowfill toggle

> close #4

> close #2-3,5-6

> hide sel surfaces

> show sel surfaces

> hide sel surfaces

> select ::name="PHE"

110 atoms, 111 bonds, 10 residues, 1 model selected  

> show sel cartoons

> show sel atoms

> show sel surfaces

> hide sel surfaces

> select add #1

1384 atoms, 1420 bonds, 173 residues, 2 models selected  

> show sel surfaces

> mlp sel

Map values for surface
"AF_Q9BTX3_F1_model_v2_1__pdb_ATOMS_section_With_ConSurf.pdb_A SES surface":
minimum -26.81, mean -1.314, maximum 22.91  
To also show corresponding color key, enter the above mlp command and add key
true  

> color bfactor sel

1384 atoms, 173 residues, 1 surfaces, atom bfactor range 1 to 9  

> coulombic sel

Coulombic values for
AF_Q9BTX3_F1_model_v2_1__pdb_ATOMS_section_With_ConSurf.pdb_A SES surface
#1.1: minimum, -12.30, mean 0.80, maximum 19.19  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp sel

Map values for surface
"AF_Q9BTX3_F1_model_v2_1__pdb_ATOMS_section_With_ConSurf.pdb_A SES surface":
minimum -26.23, mean -1.315, maximum 23.26  
To also show corresponding color key, enter the above mlp command and add key
true  

> color bfactor sel

1384 atoms, 173 residues, 1 surfaces, atom bfactor range 1 to 9  

> coulombic sel

Coulombic values for
AF_Q9BTX3_F1_model_v2_1__pdb_ATOMS_section_With_ConSurf.pdb_A SES surface
#1.1: minimum, -12.30, mean 0.80, maximum 19.19  
To also show corresponding color key, enter the above coulombic command and
add key true  

> color bfactor sel

1384 atoms, 173 residues, 1 surfaces, atom bfactor range 1 to 9  

> mlp sel

Map values for surface
"AF_Q9BTX3_F1_model_v2_1__pdb_ATOMS_section_With_ConSurf.pdb_A SES surface":
minimum -26.29, mean -1.315, maximum 23.57  
To also show corresponding color key, enter the above mlp command and add key
true  

> coulombic sel

Coulombic values for
AF_Q9BTX3_F1_model_v2_1__pdb_ATOMS_section_With_ConSurf.pdb_A SES surface
#1.1: minimum, -12.30, mean 0.80, maximum 19.19  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide sel surfaces

> show sel atoms

> color sel byhetero

> color bfactor sel

1384 atoms, 173 residues, 1 surfaces, atom bfactor range 1 to 9  

> color sel byhetero

> color bfactor sel

1384 atoms, 173 residues, 1 surfaces, atom bfactor range 1 to 9  

> color sel byhetero

> color bfactor sel

1384 atoms, 173 residues, 1 surfaces, atom bfactor range 1 to 9  

> mlp sel

Map values for surface
"AF_Q9BTX3_F1_model_v2_1__pdb_ATOMS_section_With_ConSurf.pdb_A SES surface":
minimum -26.26, mean -1.316, maximum 23.52  
To also show corresponding color key, enter the above mlp command and add key
true  

> color bfactor sel

1384 atoms, 173 residues, 1 surfaces, atom bfactor range 1 to 9  

> mlp sel

Map values for surface
"AF_Q9BTX3_F1_model_v2_1__pdb_ATOMS_section_With_ConSurf.pdb_A SES surface":
minimum -26.45, mean -1.317, maximum 22.87  
To also show corresponding color key, enter the above mlp command and add key
true  

> color bfactor sel

1384 atoms, 173 residues, 1 surfaces, atom bfactor range 1 to 9  

> mlp sel

Map values for surface
"AF_Q9BTX3_F1_model_v2_1__pdb_ATOMS_section_With_ConSurf.pdb_A SES surface":
minimum -26.65, mean -1.314, maximum 23.37  
To also show corresponding color key, enter the above mlp command and add key
true  

> color bfactor sel

1384 atoms, 173 residues, 1 surfaces, atom bfactor range 1 to 9  

> mlp sel

Map values for surface
"AF_Q9BTX3_F1_model_v2_1__pdb_ATOMS_section_With_ConSurf.pdb_A SES surface":
minimum -26.55, mean -1.315, maximum 23.66  
To also show corresponding color key, enter the above mlp command and add key
true  

> color bfactor sel

1384 atoms, 173 residues, 1 surfaces, atom bfactor range 1 to 9  

> mlp sel

Map values for surface
"AF_Q9BTX3_F1_model_v2_1__pdb_ATOMS_section_With_ConSurf.pdb_A SES surface":
minimum -26.55, mean -1.315, maximum 23.66  
To also show corresponding color key, enter the above mlp command and add key
true  

> color bfactor sel

1384 atoms, 173 residues, 1 surfaces, atom bfactor range 1 to 9  

> mlp sel

Map values for surface
"AF_Q9BTX3_F1_model_v2_1__pdb_ATOMS_section_With_ConSurf.pdb_A SES surface":
minimum -26.55, mean -1.315, maximum 23.66  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide sel surfaces

> hide sel atoms

> open /Users/hwang/Downloads/AF-Q9Y6X1-F1-model_v3.pdb

AF-Q9Y6X1-F1-model_v3.pdb title:  
Alphafold monomer V2.0 prediction for stress-associated endoplasmic reticulum
protein 1 (Q9Y6X1) [more info...]  
  
Chain information for AF-Q9Y6X1-F1-model_v3.pdb #2  
---  
Chain | Description | UniProt  
A | stress-associated endoplasmic reticulum protein 1 | SERP1_HUMAN  
  

> select add #2

1899 atoms, 1942 bonds, 239 residues, 3 models selected  

> select subtract #1

515 atoms, 522 bonds, 66 residues, 2 models selected  

> ui mousemode right rotate

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.33751,0.69654,-0.63318,-1.1708,-0.69799,0.26613,0.66482,12.541,0.63159,0.66633,0.39636,-11.375

> view matrix models
> #2,0.45745,0.86811,0.19267,-0.49523,-0.47064,0.052519,0.88076,14.037,0.75448,-0.49358,0.43259,-5.3824

> view matrix models
> #2,0.42454,0.12895,0.89618,8.7766,-0.77405,-0.46178,0.43313,15.309,0.46969,-0.87757,-0.096232,-5.5089

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.42454,0.12895,0.89618,11.914,-0.77405,-0.46178,0.43313,16.265,0.46969,-0.87757,-0.096232,8.4932

> ui mousemode right translate

Drag select of 64 residues  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for
AF_Q9BTX3_F1_model_v2_1__pdb_ATOMS_section_With_ConSurf.pdb_A SES surface
#1.1: minimum, -12.30, mean 0.80, maximum 19.19  
Coulombic values for AF-Q9Y6X1-F1-model_v3.pdb_A SES surface #2.1: minimum,
-9.38, mean 1.77, maximum 13.90  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide sel surfaces

> select #2/A:13

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

125 atoms, 125 bonds, 15 residues, 2 models selected  

> select up

515 atoms, 522 bonds, 66 residues, 2 models selected  

> mlp sel

Map values for surface "AF-Q9Y6X1-F1-model_v3.pdb_A SES surface": minimum
-25.96, mean -2.418, maximum 22.16  
To also show corresponding color key, enter the above mlp command and add key
true  

> coulombic sel

Coulombic values for AF-Q9Y6X1-F1-model_v3.pdb_A SES surface #2.1: minimum,
-9.38, mean 1.77, maximum 13.90  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide sel surfaces

[Repeated 1 time(s)]

> show sel surfaces

> hide sel surfaces

Drag select of 71 residues  

> show sel atoms

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.54073,-0.63563,-0.55099,-10.256,0.72073,-0.012309,-0.69311,3.7006,0.43378,-0.7719,0.46477,3.8983,#2,0.44158,0.67976,0.5856,6.327,-0.64842,-0.20933,0.73193,15.902,0.62013,-0.70293,0.34834,11.058

> select add #2

896 atoms, 522 bonds, 113 residues, 4 models selected  

> view matrix models
> #1,-0.54073,-0.63563,-0.55099,-10.389,0.72073,-0.012309,-0.69311,3.3174,0.43378,-0.7719,0.46477,3.4009,#2,0.44158,0.67976,0.5856,6.1942,-0.64842,-0.20933,0.73193,15.519,0.62013,-0.70293,0.34834,10.56

> view matrix models
> #1,-0.54073,-0.63563,-0.55099,-9.8669,0.72073,-0.012309,-0.69311,4.4265,0.43378,-0.7719,0.46477,5.467,#2,0.44158,0.67976,0.5856,6.7164,-0.64842,-0.20933,0.73193,16.628,0.62013,-0.70293,0.34834,12.626

> select add #1

1899 atoms, 1942 bonds, 239 residues, 4 models selected  

> select subtract #1

515 atoms, 522 bonds, 66 residues, 3 models selected  

> view matrix models
> #2,0.44158,0.67976,0.5856,10.261,-0.64842,-0.20933,0.73193,24.102,0.62013,-0.70293,0.34834,26.662

> select #1/A:165

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

127 atoms, 127 bonds, 13 residues, 2 models selected  

> select up

1384 atoms, 1420 bonds, 173 residues, 2 models selected  

> color sel byhetero

> hide #!2 models

> color bfactor sel

1384 atoms, 173 residues, 1 surfaces, atom bfactor range 1 to 9  

> mlp sel

Map values for surface
"AF_Q9BTX3_F1_model_v2_1__pdb_ATOMS_section_With_ConSurf.pdb_A SES surface":
minimum -26.07, mean -1.31, maximum 23.1  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide sel surfaces

> color sel byhetero

> show sel atoms

> show sel surfaces

> mlp sel

Map values for surface
"AF_Q9BTX3_F1_model_v2_1__pdb_ATOMS_section_With_ConSurf.pdb_A SES surface":
minimum -26.31, mean -1.316, maximum 23.27  
To also show corresponding color key, enter the above mlp command and add key
true  

> color bfactor sel

1384 atoms, 173 residues, 1 surfaces, atom bfactor range 1 to 9  

> hide sel surfaces

> color bfactor sel

1384 atoms, 173 residues, 1 surfaces, atom bfactor range 1 to 9  

> select subtract #1

1 model selected  

> select add #1

1384 atoms, 1420 bonds, 173 residues, 1 model selected  

> mlp sel

Map values for surface
"AF_Q9BTX3_F1_model_v2_1__pdb_ATOMS_section_With_ConSurf.pdb_A SES surface":
minimum -26.21, mean -1.314, maximum 23.37  
To also show corresponding color key, enter the above mlp command and add key
true  

> color bfactor sel

1384 atoms, 173 residues, 1 surfaces, atom bfactor range 1 to 9  

> hide sel surfaces

> select #1/A:163

11 atoms, 10 bonds, 1 residue, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> select #1/A:165

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:158

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

> show sel surfaces

> hide sel surfaces

> select #1/A:173

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:1-173

1384 atoms, 1420 bonds, 173 residues, 1 model selected  

> show sel surfaces

> hide sel surfaces

> show sel surfaces

> hide sel surfaces

> select #1/A:96

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:135

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

> select #1/A:104

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

> select #1/A:22

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

> select #1/A:68

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

> select add #1

1384 atoms, 1420 bonds, 173 residues, 2 models selected  

> hide sel atoms

> ui tool show "Color Actions"

[Repeated 1 time(s)]

> ui tool show "Color Key"

> ui mousemode right "color key"

> key blue:min white: #941751:max

> key #ff9300:min white: #941751:max

> select subtract #1

1 model selected  

> select add #1

1384 atoms, 1420 bonds, 173 residues, 1 model selected  

> color bfactor sel

1384 atoms, 173 residues, 1 surfaces, atom bfactor range 1 to 9  

> ui mousemode right "translate selected models"

> ui tool show "Color Key"

> ui mousemode right "color key"

> key delete

> ui mousemode right "translate selected models"

> ui tool show "Color Actions"

> ui windowfill toggle

[Repeated 1 time(s)]

> ui tool show "Color Actions"

> color byattribute seq_conservation palette cyanmaroon

1899 atoms, 239 residues, 2 surfaces, atom seq_conservation range 100 to 100  

> color bfactor sel

1384 atoms, 173 residues, 1 surfaces, atom bfactor range 1 to 9  

> color byattribute seq_conservation

1899 atoms, 239 residues, 2 surfaces, atom seq_conservation range 100 to 100  

> color bfactor sel

1384 atoms, 173 residues, 1 surfaces, atom bfactor range 1 to 9  

> select #1/A:132

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

104 atoms, 107 bonds, 13 residues, 2 models selected  

> select up

1384 atoms, 1420 bonds, 173 residues, 2 models selected  

> close session

> open
> /Users/hwang/Dropbox/Mac/Documents/Manu/TMEM208_Consurf/AF_Q9BTX3_F1_model_v2_1__pdb_ATOMS_section_With_ConSurf.pdb
> format pdb

AF_Q9BTX3_F1_model_v2_1__pdb_ATOMS_section_With_ConSurf.pdb title:  
Alphafold monomer V2.0 prediction for transmembrane protein 208 (Q9BTX3) [more
info...]  
  
Chain information for
AF_Q9BTX3_F1_model_v2_1__pdb_ATOMS_section_With_ConSurf.pdb #1  
---  
Chain | Description | UniProt  
A | transmembrane protein 208 | TM208_HUMAN  
  

> select /A:132

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

104 atoms, 107 bonds, 13 residues, 1 model selected  

> select up

1384 atoms, 1420 bonds, 173 residues, 1 model selected  

> view matrix models
> #1,0.53536,0.42836,0.72794,11.037,0.76518,0.11895,-0.63274,-0.045625,-0.35763,0.89575,-0.26409,10.996

> view matrix models
> #1,0.53536,0.42836,0.72794,-15.521,0.76518,0.11895,-0.63274,1.2499,-0.35763,0.89575,-0.26409,10.996

> select /A

1384 atoms, 1420 bonds, 173 residues, 1 model selected  

> close session

> open
> /Users/hwang/Downloads/CCT4SSSCA1RLD3_27cb1_unrelaxed_rank_1_model_2.pdb
> format pdb

Chain information for CCT4SSSCA1RLD3_27cb1_unrelaxed_rank_1_model_2.pdb #1  
---  
Chain | Description  
B | No description available  
C | No description available  
D | No description available  
  
Drag select of 1105 residues  

> ui tool show "Side View"

> view sel

> view matrix models
> #1,0.75807,-0.013915,-0.65203,1.2385,0.026569,0.9996,0.0095572,-3.7708,0.65163,-0.024569,0.75814,11.566

Drag select of 1107 residues  

> select up

8265 atoms, 8375 bonds, 1108 residues, 1 model selected  

> select up

8265 atoms, 8375 bonds, 1108 residues, 1 model selected  

> help help:contact.html

> select #1/B

4045 atoms, 4079 bonds, 539 residues, 1 model selected  

> select up

8265 atoms, 8375 bonds, 1108 residues, 1 model selected  




OpenGL version: 4.1 ATI-4.7.103
OpenGL renderer: AMD Radeon Pro 5700 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac20,2
      Processor Name: 10-Core Intel Core i9
      Processor Speed: 3.6 GHz
      Number of Processors: 1
      Total Number of Cores: 10
      L2 Cache (per Core): 256 KB
      L3 Cache: 20 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 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 12.2.1 (21D62)
      Kernel Version: Darwin 21.3.0
      Time since boot: 46 days 5:15

Graphics/Displays:

    AMD Radeon Pro 5700:

      Chipset Model: AMD Radeon Pro 5700
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x731b
      Revision ID: 0x0040
      ROM Revision: 113-D1820Q-231
      VBIOS Version: 113-D182A2XG-013
      Option ROM Version: 113-D182A2XG-013
      EFI Driver Version: 01.01.231
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          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
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    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: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    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: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    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: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    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: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    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: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    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: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    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: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    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
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
File attachment: Screenshot 2022-09-12 at 17.23.15.png

Screenshot 2022-09-12 at 17.23.15.png​

[hwang@…]

Added by email2trac

[Eric Pettersen]

Reported by Huping Wang

[Tom Goddard]

Fixed I think in tonight's daily build.

This is a graphics bug in Mac AMD Radeon Pro 5700 graphics. I've seen it in a few older Mac AMD graphics cards and have put in a work-around to fix the selection outlines by rendering them off-screen. Let me know if it works. I don't have a Mac with that graphics to test.

[hwang@…]

Dear Tom,

Thanks a lot. Now this is fixed.

All the best,
Huping

[Tom Goddard]

Thanks for telling me.