Render By Attribute generates wrong command

[migraham@…]

The following bug report has been submitted:
Platform:        macOS-15.7.7-arm64-arm-64bit
ChimeraX Version: 1.12 (2026-06-12 03:42:34 UTC)
Description
The gui tool "Render/Select by Attribute" does not work as intended when selecting by attribute using the "outside thresholds" mode. Specifically, when limiting the selection to a single model, the model selection is only applied to the lower bound critera, not the upper bound, e.g. it will execute the command "select #4@@bfactor<5.0 | @@bfactor>40.0". In this exqample, atoms with bfactor  < 5 from only #4 will be selected, but atoms from ALL models with bfactor > 40 will be selected too. Adding the '&' operator to the command executed by the gui solves this issue, e.g, "select #4&@@bfactor<5.0 | @@bfactor>40.0". This can be replicated using the attached file.

Log:
UCSF ChimeraX version: 1.12 (2026-06-12)  
© 2016-2026 Regents of the University of California. All rights reserved.  

> surface cap false

Log from Thu Aug 6 11:56:19 2026UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/sir_mr_dog/Documents/Grad School/Borgstahl Lab/SSRL Data/June
> 2025/FeSOD2_QM/Fe_red/tddft/B3LYP/wat2_wiggle/out.wat2-wall_opt-
> tddft_ls/tddft/wat2-wall_tddft_ls.out"

Opened wat2-wall_tddft_ls.out as an ORCA output file  

> ui tool show "Orbital Viewer"

0.517455424  
(6895277, 1160391666)  
Opened MO beta 224 as #1.2, grid size 107,97,82, pixel 0.202,0.201,0.201,
shown at level -0.05,0.05, step 1, values float64  

> hide #1.2

0.517455424  
(6823928, 1167124725)  
Opened MO beta 225 as #1.3, grid size 107,97,82, pixel 0.202,0.201,0.201,
shown at level -0.05,0.05, step 1, values float64  

> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl Lab/SSRL Data/June
> 2025/FeSOD2_QM/Fe_red/tddft/B3LYP/wat2_wiggle/out.wat2-wall_opt-
> tddft_ls/tddft/Images/Lb+2.png" width 935 height 859 supersample 3

> hide #1.3

0.517455424  
(6817600, 1173926645)  
Opened MO beta 228 as #1.4, grid size 107,97,82, pixel 0.202,0.201,0.201,
shown at level -0.05,0.05, step 1, values float64  

> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl Lab/SSRL Data/June
> 2025/FeSOD2_QM/Fe_red/tddft/B3LYP/wat2_wiggle/out.wat2-wall_opt-
> tddft_ls/tddft/Images/Lb+5.png" width 1109 height 859 supersample 3

> hide #1.4

0.517455424  
(6815224, 1187539421)  
Opened MO beta 229 as #1.5, grid size 107,97,82, pixel 0.202,0.201,0.201,
shown at level -0.05,0.05, step 1, values float64  

> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl Lab/SSRL Data/June
> 2025/FeSOD2_QM/Fe_red/tddft/B3LYP/wat2_wiggle/out.wat2-wall_opt-
> tddft_ls/tddft/Images/Lb+6.png" width 1109 height 859 supersample 3

> hide #1.5

0.517455424  
(6815160, 1146686945)  
Opened MO alpha 223 as #1.6, grid size 107,97,82, pixel 0.202,0.201,0.201,
shown at level -0.05,0.05, step 1, values float64  

> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl Lab/SSRL Data/June
> 2025/FeSOD2_QM/Fe_red/tddft/B3LYP/wat2_wiggle/out.wat2-wall_opt-
> tddft_ls/tddft/Images/La.png" width 1109 height 859 supersample 3

> hide #1.6

0.517455424  
(6814840, 1194348185)  
Opened MO beta 223 as #1.7, grid size 107,97,82, pixel 0.202,0.201,0.201,
shown at level -0.05,0.05, step 1, values float64  

> show #1.6

> volume #1.6 level -0.050 level 0.050 color #0433ff80 color #00fdff80

> hide #1.7

> hide #1.6

0.517455424  
(6820344, 1160310033)  
Opened MO alpha 224 as #1.8, grid size 107,97,82, pixel 0.202,0.201,0.201,
shown at level -0.05,0.05, step 1, values float64  

> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl Lab/SSRL Data/June
> 2025/FeSOD2_QM/Fe_red/tddft/B3LYP/wat2_wiggle/out.wat2-wall_opt-
> tddft_ls/tddft/Images/La+1.png" width 1109 height 859 supersample 3

> hide #1.8

0.517455424  
(6814808, 1139878181)  
Opened MO alpha 226 as #1.9, grid size 107,97,82, pixel 0.202,0.201,0.201,
shown at level -0.05,0.05, step 1, values float64  

> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl Lab/SSRL Data/June
> 2025/FeSOD2_QM/Fe_red/tddft/B3LYP/wat2_wiggle/out.wat2-wall_opt-
> tddft_ls/tddft/Images/La+3.png" width 1109 height 859 supersample 3

> hide #1.9

0.517455424  
(6814992, 1160306445)  
Opened MO beta 231 as #1.10, grid size 107,97,82, pixel 0.202,0.201,0.201,
shown at level -0.05,0.05, step 1, values float64  

> show #1.10

> volume #1.10 level -0.050 level 0.050 color #0433ff80 color #00fdff80

> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl Lab/SSRL Data/June
> 2025/FeSOD2_QM/Fe_red/tddft/B3LYP/wat2_wiggle/out.wat2-wall_opt-
> tddft_ls/tddft/Images/Lb+8.png" width 1109 height 859 supersample 3

> hide #1.10

0.517455424  
(6815240, 1173923413)  
Opened MO alpha 232 as #1.11, grid size 107,97,82, pixel 0.202,0.201,0.201,
shown at level -0.05,0.05, step 1, values float64  

> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl Lab/SSRL Data/June
> 2025/FeSOD2_QM/Fe_red/tddft/B3LYP/wat2_wiggle/out.wat2-wall_opt-
> tddft_ls/tddft/Images/La+9.png" width 1109 height 859 supersample 3

> hide #1.11

0.517455424  
(6815352, 1139880042)  
Opened MO beta 233 as #1.12, grid size 107,97,82, pixel 0.202,0.201,0.201,
shown at level -0.05,0.05, step 1, values float64  

> hide #1.12

0.517455424  
(6815072, 1139879787)  
Opened MO alpha 234 as #1.13, grid size 107,97,82, pixel 0.202,0.201,0.201,
shown at level -0.05,0.05, step 1, values float64  

> open "/Users/sir_mr_dog/Documents/Grad School/Borgstahl Lab/SSRL Data/June
> 2025/FeSOD2_QM/Fe_red/tddft/B3LYP/wat1_wiggle/out.wat1-wall_opt-
> tddft/tddft/output/wat1-wall_tddft.out"

Opened wat1-wall_tddft.out as an ORCA output file  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

0.517455424  
(6821344, 1139797226)  
Opened MO beta 216 as #2.2, grid size 107,97,82, pixel 0.202,0.201,0.2, shown
at level -0.05,0.05, step 1, values float64  

> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl Lab/SSRL Data/June
> 2025/FeSOD2_QM/Fe_red/tddft/B3LYP/wat1_wiggle/out.wat1-wall_opt-
> tddft/tddft/orbital_imgs/Lb.png" width 1109 height 859 supersample 3

> hide #2.2

0.517455424  
(6821640, 1112560866)  
Opened MO beta 219 as #2.3, grid size 107,97,82, pixel 0.202,0.201,0.2, shown
at level -0.05,0.05, step 1, values float64  

> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl Lab/SSRL Data/June
> 2025/FeSOD2_QM/Fe_red/tddft/B3LYP/wat1_wiggle/out.wat1-wall_opt-
> tddft/tddft/orbital_imgs/Lb+3.png" width 1109 height 859 supersample 3

> hide #2.3

0.517455424  
(6815160, 1098937475)  
Opened MO beta 217 as #2.4, grid size 107,97,82, pixel 0.202,0.201,0.2, shown
at level -0.05,0.05, step 1, values float64  

> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl Lab/SSRL Data/June
> 2025/FeSOD2_QM/Fe_red/tddft/B3LYP/wat1_wiggle/out.wat1-wall_opt-
> tddft/tddft/orbital_imgs/Lb+1.png" width 1109 height 859 supersample 3

> hide #2.4

0.517455424  
(6815576, 1119364899)  
Opened MO beta 218 as #2.5, grid size 107,97,82, pixel 0.202,0.201,0.2, shown
at level -0.05,0.05, step 1, values float64  

> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl Lab/SSRL Data/June
> 2025/FeSOD2_QM/Fe_red/tddft/B3LYP/wat1_wiggle/out.wat1-wall_opt-
> tddft/tddft/orbital_imgs/Lb+2.png" width 1109 height 859 supersample 3

> hide #2.5

0.517455424  
(6814896, 1098937578)  
Opened MO beta 238 as #2.6, grid size 107,97,82, pixel 0.202,0.201,0.2, shown
at level -0.05,0.05, step 1, values float64  

> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl Lab/SSRL Data/June
> 2025/FeSOD2_QM/Fe_red/tddft/B3LYP/wat1_wiggle/out.wat1-wall_opt-
> tddft/tddft/orbital_imgs/Lb+22.png" width 1109 height 859 supersample 3

> hide #2.6

0.517455424  
(6815128, 1119428506)  
Opened MO beta 239 as #2.7, grid size 107,97,82, pixel 0.202,0.201,0.2, shown
at level -0.05,0.05, step 1, values float64  

> show #2.7

> volume #2.7 level -0.050 level 0.050 color #0433ff80 color #00fdff80

> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl Lab/SSRL Data/June
> 2025/FeSOD2_QM/Fe_red/tddft/B3LYP/wat1_wiggle/out.wat1-wall_opt-
> tddft/tddft/orbital_imgs/Lb+23.png" width 1109 height 859 supersample 3

> hide #2.7

0.517455424  
(6815856, 1092130306)  
Opened MO beta 235 as #2.8, grid size 107,97,82, pixel 0.202,0.201,0.2, shown
at level -0.05,0.05, step 1, values float64  

> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl Lab/SSRL Data/June
> 2025/FeSOD2_QM/Fe_red/tddft/B3LYP/wat1_wiggle/out.wat1-wall_opt-
> tddft/tddft/orbital_imgs/Lb+19.png" width 1109 height 859 supersample 3

> hide #2.8

0.517455424  
(6814808, 1105746022)  
Opened MO alpha 222 as #2.9, grid size 107,97,82, pixel 0.202,0.201,0.2, shown
at level -0.05,0.05, step 1, values float64  

> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl Lab/SSRL Data/June
> 2025/FeSOD2_QM/Fe_red/tddft/B3LYP/wat1_wiggle/out.wat1-wall_opt-
> tddft/tddft/orbital_imgs/La+2.png" width 1109 height 859 supersample 3

> hide #2.9

0.517455424  
(6813248, 1139788186)  
Opened MO alpha 224 as #2.10, grid size 107,97,82, pixel 0.202,0.201,0.2,
shown at level -0.05,0.05, step 1, values float64  

> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl Lab/SSRL Data/June
> 2025/FeSOD2_QM/Fe_red/tddft/B3LYP/wat1_wiggle/out.wat1-wall_opt-
> tddft/tddft/orbital_imgs/La+4.png" width 1109 height 859 supersample 3

> hide #2.10

0.517455424  
(6815104, 1098937458)  
Opened MO alpha 225 as #2.11, grid size 107,97,82, pixel 0.202,0.201,0.2,
shown at level -0.05,0.05, step 1, values float64  

> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl Lab/SSRL Data/June
> 2025/FeSOD2_QM/Fe_red/tddft/B3LYP/wat1_wiggle/out.wat1-wall_opt-
> tddft/tddft/orbital_imgs/La+5.png" width 1109 height 859 supersample 3

> hide #2.11

0.517455424  
(6814872, 1105746658)  
Opened MO alpha 226 as #2.12, grid size 107,97,82, pixel 0.202,0.201,0.2,
shown at level -0.05,0.05, step 1, values float64  

> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl Lab/SSRL Data/June
> 2025/FeSOD2_QM/Fe_red/tddft/B3LYP/wat1_wiggle/out.wat1-wall_opt-
> tddft/tddft/orbital_imgs/La+6.png" width 1109 height 859 supersample 3

> show #2.12

> volume #2.12 level -0.050 level 0.050 color #0433ff80 color #00fdff80

> hide #2.12

0.517455424  
(6815800, 1092262234)  
Opened MO alpha 228 as #2.13, grid size 107,97,82, pixel 0.202,0.201,0.2,
shown at level -0.05,0.05, step 1, values float64  

> save "/Users/sir_mr_dog/Documents/Grad School/Borgstahl Lab/SSRL Data/June
> 2025/FeSOD2_QM/Fe_red/tddft/B3LYP/wat1_wiggle/out.wat1-wall_opt-
> tddft/tddft/orbital_imgs/La+8.png" width 1109 height 859 supersample 3

> hide #2.1 models

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> hide #!1 models

> hide #!2.13 models

> select clear

> open "/Users/sir_mr_dog/Library/CloudStorage/OneDrive-
> UniversityofNebraskaMedicalCenter/Borgstahl Lab/ORNL
> Data/Jun_2026/Reduced/X-ray/Only monomer.pdb"

Chain information for Only monomer.pdb #3  
---  
Chain | Description  
A | No description available  
  
24 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Computing secondary structure  

> move cofr #3

> cofr 0,0,0

> move cofr #3

> style #3#!2 stick

Changed 3212 atom styles  

> hide #!2 models

> hide #3 cartoons

> show #3 cartoons

> style #3 stick

Changed 3095 atom styles  

> hide #3 cartoons

> style #3 stick

Changed 3095 atom styles  

> show #3 atoms

> delete atoms @H

> delete atoms H

> select clear

> save "/Users/sir_mr_dog/Library/CloudStorage/OneDrive-
> UniversityofNebraskaMedicalCenter/Borgstahl Lab/ORNL
> Data/Jun_2026/Reduced/X-ray/min_monomer.pdb" models #3

> open "/Users/sir_mr_dog/Library/CloudStorage/OneDrive-
> UniversityofNebraskaMedicalCenter/Borgstahl Lab/ORNL
> Data/Jun_2026/Reduced/X-ray/min_monomer.pdb"

Chain information for min_monomer.pdb #4  
---  
Chain | Description  
A | No description available  
  
9 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> save "/Users/sir_mr_dog/Library/CloudStorage/OneDrive-
> UniversityofNebraskaMedicalCenter/Borgstahl Lab/ORNL
> Data/Jun_2026/Reduced/X-ray/only_monomer.xyz" models #4 coordsets false
> append false

> hide #4 models

> show #4 models

> hide #3 models

> show #!2 models

> hide #!2 models

> show #3 models

> show #!2 models

> hide #!2 models

> close session

> open "/Users/sir_mr_dog/Library/CloudStorage/OneDrive-
> UniversityofNebraskaMedicalCenter/Borgstahl Lab/ORNL
> Data/Jun_2026/Reduced/X-ray/phaser_7/X-ray_red_phaser.1.pdb"
> "/Users/sir_mr_dog/Library/CloudStorage/OneDrive-
> UniversityofNebraskaMedicalCenter/Borgstahl Lab/ORNL
> Data/Jun_2026/Reduced/X-ray/phaser_7/X-ray_red_phaser.2.pdb"
> "/Users/sir_mr_dog/Library/CloudStorage/OneDrive-
> UniversityofNebraskaMedicalCenter/Borgstahl Lab/ORNL
> Data/Jun_2026/Reduced/X-ray/phaser_7/X-ray_red_phaser.3.pdb"

Summary of feedback from opening
/Users/sir_mr_dog/Library/CloudStorage/OneDrive-
UniversityofNebraskaMedicalCenter/Borgstahl Lab/ORNL
Data/Jun_2026/Reduced/X-ray/phaser_7/X-ray_red_phaser.1.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK TITLE Use all monomer ensemmble  
  
Ignored bad PDB record found on line 2  
REMARK Log-Likelihood Gain: 13888.957  
  
Ignored bad PDB record found on line 3  
REMARK RFZ=4.2 TFZ=14.8 PAK=0 LLG=242 TFZ==17.2 RFZ=5.2 TFZ=46.4 PAK=0
LLG=1743 TFZ==48.9 LLG=13889 TFZ==119.6  
  
Ignored bad PDB record found on line 4  
REMARK ENSEMBLE monomers EULER 191.61 0.41 348.20 FRAC -0.362 0.154 0.058  
  
Ignored bad PDB record found on line 5  
REMARK ENSEMBLE monomers EULER 301.54 159.01 61.34 FRAC 0.074 0.409 0.127  
  
Summary of feedback from opening
/Users/sir_mr_dog/Library/CloudStorage/OneDrive-
UniversityofNebraskaMedicalCenter/Borgstahl Lab/ORNL
Data/Jun_2026/Reduced/X-ray/phaser_7/X-ray_red_phaser.2.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK TITLE Use all monomer ensemmble  
  
Ignored bad PDB record found on line 2  
REMARK RFZ=4.2 TFZ=14.8 PAK=0 LLG=242 TFZ==17.2 RFZ=5.2 TFZ=46.4 PAK=0  
  
Ignored bad PDB record found on line 3  
REMARK ENSEMBLE monomers EULER 64.48 0.30 114.95 FRAC -0.362 0.153 0.058  
  
Ignored bad PDB record found on line 4  
REMARK ENSEMBLE monomers EULER 299.90 159.40 61.06 FRAC 0.072 0.408 0.126  
  
Summary of feedback from opening
/Users/sir_mr_dog/Library/CloudStorage/OneDrive-
UniversityofNebraskaMedicalCenter/Borgstahl Lab/ORNL
Data/Jun_2026/Reduced/X-ray/phaser_7/X-ray_red_phaser.3.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK TITLE Use all monomer ensemmble  
  
Ignored bad PDB record found on line 2  
REMARK Log-Likelihood Gain: 91.435  
  
Ignored bad PDB record found on line 3  
REMARK RFZ=4.2 TFZ=8.2 PAK=3 LLG=91 TFZ==9.9  
  
Ignored bad PDB record found on line 4  
REMARK ENSEMBLE monomers EULER 62.64 0.85 117.31 FRAC -0.363 0.152 0.093  
  
Chain information for X-ray_red_phaser.1.pdb #1  
---  
Chain | Description  
A B | No description available  
  
Chain information for X-ray_red_phaser.2.pdb #2  
---  
Chain | Description  
A B | No description available  
  
Chain information for X-ray_red_phaser.3.pdb #3  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  
[Repeated 2 time(s)]

> hide #1 models

> hide #2 models

> hide #3 models

> show #3 models

> hide #3 models

> show #1 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> close #2

> close #3

> ui tool show "Crystal Contacts"

> crystalcontacts #1 distance 1

2 pairs of asymmetric units of X-ray_red_phaser.1.pdb contact at distance 1.0
A

    
    
      Atoms  MTRIX  SMTRY   Unit cell  MTRIXref  Copies
         4     0      6     -1  0  0      0         1
         3     0      6      0  1  0      0         1
    

  

> crystalcontacts #1 distance 2

5 pairs of asymmetric units of X-ray_red_phaser.1.pdb contact at distance 2.0
A

    
    
      Atoms  MTRIX  SMTRY   Unit cell  MTRIXref  Copies
        12     0      6      0  1  0      0         1
        12     0      6     -1  0  0      0         1
         9     0     11      0  1  0      0         1
         2     0      5      1  1  0      0         1
         2     0      4     -1  0 -1      0         1
    

  

> crystalcontacts delete #1

> crystalcontacts #1 distance 2

5 pairs of asymmetric units of X-ray_red_phaser.1.pdb contact at distance 2.0
A

    
    
      Atoms  MTRIX  SMTRY   Unit cell  MTRIXref  Copies
        12     0      6      0  1  0      0         1
        12     0      6     -1  0  0      0         1
         9     0     11      0  1  0      0         1
         2     0      5      1  1  0      0         1
         2     0      4     -1  0 -1      0         1
    

  

> select add #1

6190 atoms, 6282 bonds, 396 residues, 1 model selected  

> ui tool show "Color Actions"

> ui tool show "Render/Select by Attribute"

> select clear

> select #2.3/B:34

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

348 atoms, 351 bonds, 22 residues, 1 model selected  

> select up

3095 atoms, 3141 bonds, 198 residues, 1 model selected  

> select up

6190 atoms, 6282 bonds, 396 residues, 1 model selected  

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> select add #2.1

6190 atoms, 6282 bonds, 396 residues, 1 model selected  

> select subtract #2.1

Nothing selected  

> select add #2.3

6190 atoms, 6282 bonds, 396 residues, 1 model selected  

> select subtract #2.3

Nothing selected  

> close #2.1-2,4-5

> ui tool show "Render/Select by Attribute"

> color byattribute a:bfactor #1#2.3 target cabs palette
> 4.28,blue:20.7626,white:65.5486,red

12380 atoms, 792 residues, atom bfactor range 4.28 to 130  

> show atoms

> hide #!2 models

> show #!2 models

> hide #!2 models

> select #1/B:105@HB3

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

213 atoms, 214 bonds, 13 residues, 1 model selected  

> select up

3095 atoms, 3141 bonds, 198 residues, 1 model selected  

> delete atoms sel

> show #!2 models

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select up

160 atoms, 162 bonds, 9 residues, 1 model selected  

> select up

3095 atoms, 3141 bonds, 198 residues, 1 model selected  

> delete atoms sel

> ui tool show "Render/Select by Attribute"

> select #1#2.3@@bfactor<4.28000020980835 | @@bfactor>72.93900432861028

3147 atoms, 3167 bonds, 206 residues, 2 models selected  

> hide sel cartoons

> select clear

> combine #1#2.3

> hide #1 models

> hide #2.3 models

> hide #!2 models

> select add #3

6190 atoms, 6282 bonds, 396 residues, 1 model selected  

> select subtract #3

Nothing selected  

> ui tool show "Render/Select by Attribute"

> select #3@@bfactor<4.28000020980835 | @@bfactor>71.9045781358423

188 atoms, 88 bonds, 30 residues, 3 models selected  

> delete atoms sel

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

18 atoms, 17 bonds, 1 residue, 1 model selected  

> delete atoms sel

> select clear

> ui tool show "Render/Select by Attribute"

> color byattribute a:bfactor #3 target cabs palette
> 4.28,blue:18.513,white:52.5484,red

6078 atoms, 393 residues, atom bfactor range 4.28 to 71.3  

> ui tool show "Render/Select by Attribute"

> select #3@@bfactor<4.28000020980835 | @@bfactor>59.59474183060961

209 atoms, 26 bonds, 55 residues, 3 models selected  

> hide sel & #3 cartoons

> select up

998 atoms, 947 bonds, 55 residues, 3 models selected  

> select up

5391 atoms, 5435 bonds, 347 residues, 3 models selected  

> hide sel & #3 cartoons

> select down

998 atoms, 947 bonds, 55 residues, 3 models selected  

> select down

209 atoms, 26 bonds, 55 residues, 3 models selected  

> select up

998 atoms, 947 bonds, 55 residues, 3 models selected  

> delete atoms sel & sideonly

> select up

4718 atoms, 4764 bonds, 347 residues, 3 models selected  

> select down

325 atoms, 276 bonds, 55 residues, 3 models selected  

> select down

325 atoms, 276 bonds, 55 residues, 3 models selected  

> select down

325 atoms, 276 bonds, 55 residues, 3 models selected  

> select down

325 atoms, 276 bonds, 55 residues, 3 models selected  

> select clear

> select #3:0

Nothing selected  

> select #3:1

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #3:1

5 atoms, 4 bonds, 1 residue, 1 model selected  

> delete atoms sel

> select H

5540 atoms, 786 residues, 3 models selected  

> delete atoms sel

> select clear

> hide #3 cartoons

> show #!2 models

> hide #!2 models

> select H

Nothing selected  

> select #3:179

10 atoms, 8 bonds, 2 residues, 1 model selected  

> view sel

> select #3:198

Nothing selected  

> select #3:197

8 atoms, 6 bonds, 2 residues, 1 model selected  

> select #3:196-197

20 atoms, 18 bonds, 4 residues, 1 model selected  

> select #3:197

8 atoms, 6 bonds, 2 residues, 1 model selected  

> delete atoms sel

> ui tool show "Render/Select by Attribute"

> select #3@@bfactor<4.28000020980835 | @@bfactor>43.06608217053068

122 atoms, 63 bonds, 54 residues, 3 models selected  

> select #3@@bfactor<4.28000020980835 | @@bfactor>37.419604747599735

276 atoms, 180 bonds, 100 residues, 3 models selected  

> select up

764 atoms, 690 bonds, 100 residues, 3 models selected  

> select #3@@bfactor<4.28000020980835 | @@bfactor>40.0

200 atoms, 118 bonds, 84 residues, 3 models selected  

> select #3@@bfactor<4.28000020980835 | @@bfactor>37.07219689181358

284 atoms, 188 bonds, 102 residues, 3 models selected  

> select #3@@bfactor<4.28000020980835 | @@bfactor>35.60829533772042

342 atoms, 226 bonds, 122 residues, 3 models selected  

> select #3@@bfactor<4.28000020980835 | @@bfactor>35.0

368 atoms, 250 bonds, 126 residues, 3 models selected  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 779, in _set_value_cb  
v = eval(val_text)  
^^^^^^^^^^^^^^  
File "<string>", line 0  
  
SyntaxError: invalid syntax  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 781, in _set_value_cb  
raise ValueError("Invalid histogram value")  
ValueError: Invalid histogram value  
  
ValueError: Invalid histogram value  
  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/histogram.py", line 781, in _set_value_cb  
raise ValueError("Invalid histogram value")  
  
See log for complete Python traceback.  
  

> delete atoms sel

> select #!3@@bfactor<3.437083403269449 | @@bfactor>35.0

Nothing selected  

> combine #1#2.3 name pruned

> close #3

> combine #1#2.3 name unpruned

> hide #!3 models

> select add #4

2790 atoms, 2857 bonds, 9 pseudobonds, 385 residues, 2 models selected  

> show sel cartoons

> hide sel cartoons

> ui tool show "Render/Select by Attribute"

> color byattribute a:bfactor #!4 target cabs palette
> 4.28,blue:19.64,white:35,red

2790 atoms, 385 residues, atom bfactor range 4.28 to 35  

> show #!1 models

> show #!2 models

> hide #!2 models

> hide #!1 models

> hide #!4 models

> select subtract #4

Nothing selected  

> show #!2 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> show #!2.3 models

> hide #!2 models

> show #!2 models

> close session

> open "/Users/sir_mr_dog/Library/CloudStorage/OneDrive-
> UniversityofNebraskaMedicalCenter/Borgstahl Lab/ORNL
> Data/Jun_2026/Reduced/X-ray/phaser_7/X-ray_red_phaser.1.pdb"

Summary of feedback from opening
/Users/sir_mr_dog/Library/CloudStorage/OneDrive-
UniversityofNebraskaMedicalCenter/Borgstahl Lab/ORNL
Data/Jun_2026/Reduced/X-ray/phaser_7/X-ray_red_phaser.1.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK TITLE Use all monomer ensemmble  
  
Ignored bad PDB record found on line 2  
REMARK Log-Likelihood Gain: 13888.957  
  
Ignored bad PDB record found on line 3  
REMARK RFZ=4.2 TFZ=14.8 PAK=0 LLG=242 TFZ==17.2 RFZ=5.2 TFZ=46.4 PAK=0
LLG=1743 TFZ==48.9 LLG=13889 TFZ==119.6  
  
Ignored bad PDB record found on line 4  
REMARK ENSEMBLE monomers EULER 191.61 0.41 348.20 FRAC -0.362 0.154 0.058  
  
Ignored bad PDB record found on line 5  
REMARK ENSEMBLE monomers EULER 301.54 159.01 61.34 FRAC 0.074 0.409 0.127  
  
Chain information for X-ray_red_phaser.1.pdb #1  
---  
Chain | Description  
A B | No description available  
  
Computing secondary structure  

> ui tool show "Crystal Contacts"

> crystalcontacts #1

7 pairs of asymmetric units of X-ray_red_phaser.1.pdb contact at distance 3.0
A

    
    
      Atoms  MTRIX  SMTRY   Unit cell  MTRIXref  Copies
       331     0     11      0  1  0      0         1
        40     0      6     -1  0  0      0         1
        25     0      6      0  1  0      0         1
        25     0      4     -1  0 -1      0         1
        22     0      5      1  1  0      0         1
         7     0     11      1  1  0      0         1
         6     0     11     -1  0  0      0         1
    

  

> close #2.2-7

> delete atoms H

> select clear

> show atoms

> select clear

> ui tool show "Render/Select by Attribute"

> color byattribute a:bfactor #1#2.1 target cabs palette
> 4.28,blue:56.52,white:108.76,red

6284 atoms, 792 residues, atom bfactor range 4.28 to 109  

> ui tool show "Render/Select by Attribute"

> color byattribute a:bfactor #1#2.1 target cabs palette
> 4.28,blue:17.509,white:45.9948,red

6284 atoms, 792 residues, atom bfactor range 4.28 to 109  

> ui tool show "Render/Select by Attribute"

> color byattribute a:bfactor #1#2.1 target cabs palette
> 4.28,blue:20,white:45,red

6284 atoms, 792 residues, atom bfactor range 4.28 to 109  

> color byattribute a:bfactor #1#2.1 target cabs palette
> 4.28,blue:20,white:50,red

6284 atoms, 792 residues, atom bfactor range 4.28 to 109  

> select #1#2.1@@bfactor<4.28000020980835 | @@bfactor>45.0

3298 atoms, 3336 bonds, 448 residues, 2 models selected  

> hide sel cartoons

> select #1#2.1@@bfactor<4.28000020980835 | @@bfactor>49.99999999999999

3261 atoms, 3307 bonds, 437 residues, 2 models selected  

> select clear

> select #1#2.1@@bfactor<4.28000020980835 | @@bfactor>49.999999999999986

3261 atoms, 3307 bonds, 437 residues, 2 models selected  

> select #1#2.1@@bfactor<4.28000020980835 | @@bfactor>60.0

3194 atoms, 3263 bonds, 417 residues, 2 models selected  

> select clear

> select #1#2.1@@bfactor<4.28000020980835 | @@bfactor>60.0

3194 atoms, 3263 bonds, 417 residues, 2 models selected  

> select subtract #1

52 atoms, 29 bonds, 21 residues, 1 model selected  

> select add #1

3194 atoms, 3263 bonds, 417 residues, 2 models selected  

> select subtract #1

52 atoms, 29 bonds, 21 residues, 1 model selected  

> select add #1

3194 atoms, 3263 bonds, 417 residues, 2 models selected  

> select subtract #1

52 atoms, 29 bonds, 21 residues, 1 model selected  

> select add #2

3142 atoms, 3234 bonds, 396 residues, 2 models selected  

> select subtract #2

Nothing selected  

> combine #1#2.1 unpruned

Expected a keyword  

> combine #1#2.1 name unpruned

Remapping chain ID 'A' in X-ray_red_phaser.1.pdb 0 1 0 sym 11 #2.1 to 'C'  
Remapping chain ID 'B' in X-ray_red_phaser.1.pdb 0 1 0 sym 11 #2.1 to 'D'  

> combine #1#2.1 name pruned

Remapping chain ID 'A' in X-ray_red_phaser.1.pdb 0 1 0 sym 11 #2.1 to 'C'  
Remapping chain ID 'B' in X-ray_red_phaser.1.pdb 0 1 0 sym 11 #2.1 to 'D'  

> select #4@@bfactor<4.28000020980835 | @@bfactor>60.0

312 atoms, 174 bonds, 126 residues, 4 models selected  

> select add #1

3402 atoms, 3379 bonds, 501 residues, 4 models selected  

> select subtract #1

260 atoms, 145 bonds, 105 residues, 3 models selected  

> select add #3

6440 atoms, 6555 bonds, 855 residues, 3 models selected  

> select add #2

9530 atoms, 9760 bonds, 1230 residues, 4 models selected  

> select subtract #2

6388 atoms, 6526 bonds, 834 residues, 2 models selected  

> select subtract #3

104 atoms, 58 bonds, 42 residues, 1 model selected  

> select #4@@bfactor<4.28000020980835 | @@bfactor>60.0

312 atoms, 174 bonds, 126 residues, 4 models selected  

> select clear

> hide #1 models

> hide #!2 models

> hide #3 models

> select #4@@bfactor<4.28000020980835 | @@bfactor>60.0

312 atoms, 174 bonds, 126 residues, 4 models selected  

> hide #4 models

> show #3 models

> hide #3 models

> show #4 models

> hide #4 models

> show #3 models

> hide #3 models

> show #4 models

> select #1@@bfactor<4.28000020980835 | @@bfactor>60.0

312 atoms, 174 bonds, 126 residues, 4 models selected  

> select #1@@bfactor<4.28000020980835 | @@bfactor>60.0

312 atoms, 174 bonds, 126 residues, 4 models selected  

> select #2.1@@bfactor<4.28000020980835 | @@bfactor>60.0

312 atoms, 174 bonds, 126 residues, 4 models selected  

> select clear

> select #1@@bfactor<4.28000020980835 | @@bfactor>60.0

312 atoms, 174 bonds, 126 residues, 4 models selected  

> select #2.1@@bfactor<4.28000020980835 | @@bfactor>60.0

312 atoms, 174 bonds, 126 residues, 4 models selected  

> hide #4 models

> show #1 models

> show #!2 models

> hide #!2 models

> hide #1 models

> show #!2 models

> hide #!2 models

> show #1 models

> show #!2 models

> select clear

> show #1#2.1 cartoons

> hide #1#2.1 atoms

> select #1/A:36

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

> select up

179 atoms, 182 bonds, 22 residues, 1 model selected  

> select up

1571 atoms, 1617 bonds, 198 residues, 1 model selected  

> select add #2.1/B:46

1580 atoms, 1625 bonds, 199 residues, 2 models selected  

> select up

1750 atoms, 1799 bonds, 220 residues, 2 models selected  

> select up

3142 atoms, 3234 bonds, 396 residues, 2 models selected  

> select up

6284 atoms, 6468 bonds, 792 residues, 2 models selected  

> select down

3142 atoms, 3234 bonds, 396 residues, 2 models selected  

> select ~sel & ##selected

3142 atoms, 3234 bonds, 396 residues, 2 models selected  

> delete atoms sel

> close #3-4

> combine #1#2.1 name unpruned

> combine #1#2.1 name pruned

> hide #1 models

> hide #!2 models

> hide #3 models

> select add #4

3142 atoms, 3234 bonds, 396 residues, 1 model selected  

> hide sel cartoons

> show sel atoms

> select #4@@bfactor<4.28000020980835 | @@bfactor>60.0

156 atoms, 87 bonds, 63 residues, 4 models selected  

> select #4@@bfactor<4.280 | #4@@bfactor>60.0

52 atoms, 29 bonds, 21 residues, 1 model selected  

> select up

187 atoms, 168 bonds, 21 residues, 1 model selected  

> select down

52 atoms, 29 bonds, 21 residues, 1 model selected  

> select up

187 atoms, 168 bonds, 21 residues, 1 model selected  

> delete atoms sel & sideonly

> select ~sel & ##selected

2955 atoms, 3066 bonds, 375 residues, 1 model selected  

> select ~sel & ##selected

84 atoms, 65 bonds, 21 residues, 1 model selected  

> select down

84 atoms, 65 bonds, 21 residues, 1 model selected  

> select #4@@bfactor<4.28000020980835 | @@bfactor>60.0

116 atoms, 66 bonds, 47 residues, 4 models selected  

> select #4@@bfactor<4.280 | #4@@bfactor>60.0

12 atoms, 8 bonds, 5 residues, 1 model selected  

> select clear

> select #4@@bfactor<4.280 | #4@@bfactor>60.0

12 atoms, 8 bonds, 5 residues, 1 model selected  

> select #4@@bfactor<4.280 | @@bfactor>60.0

116 atoms, 66 bonds, 47 residues, 4 models selected  

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> select #4@@bfactor<4.280 | #4@@bfactor>60.0

12 atoms, 8 bonds, 5 residues, 1 model selected  

> select up

20 atoms, 17 bonds, 5 residues, 1 model selected  

> delete atoms sel

> select #4@@bfactor<4.2800002098083505 | @@bfactor>34.080032360423665

920 atoms, 690 bonds, 249 residues, 4 models selected  

> select #4@@bfactor<4.280 | #4@@bfactor>34.0

234 atoms, 164 bonds, 75 residues, 1 model selected  

> select #4@@bfactor<4.280 | #4@@bfactor>35.0

213 atoms, 145 bonds, 71 residues, 1 model selected  

> select #4@@bfactor<4.280 | #4@@bfactor>34.0

234 atoms, 164 bonds, 75 residues, 1 model selected  

> select #4@@bfactor<4.280 | #4@@bfactor>35.0

213 atoms, 145 bonds, 71 residues, 1 model selected  

> select #4@@bfactor<4.280 | #4@@bfactor>40.0

122 atoms, 73 bonds, 50 residues, 1 model selected  

> select up

414 atoms, 378 bonds, 50 residues, 1 model selected  

> select intersect sideonly

214 atoms, 170 bonds, 45 residues, 1 model selected  

> select intersect #4@@bfactor<4.280 | #4@@bfactor>35

141 atoms, 96 bonds, 44 residues, 1 model selected  

> select up

389 atoms, 354 bonds, 44 residues, 1 model selected  

> select intersect #4@@bfactor<4.280 | #4@@bfactor>34 & sideonly

146 atoms, 102 bonds, 44 residues, 1 model selected  

> delete atoms sel

> select #4@@bfactor>=50.5745447287054 & @@bfactor<=59.81094093129127

5 atoms, 2 bonds, 3 residues, 1 model selected  

> select up

13 atoms, 10 bonds, 3 residues, 1 model selected  

> delete atoms sel

> select #4/A:10@OD1

1 atom, 1 residue, 1 model selected  

> select up

6 atoms, 4 bonds, 1 residue, 1 model selected  

> select clear

> select #4/A:10@OD1

1 atom, 1 residue, 1 model selected  

> delete atoms sel

> show #4 cartoons

> select clear

> select intersect #4@@neighbor=1

Nothing selected  

> select intersect #4@@neighbors=1

Nothing selected  

> select clear

[Repeated 1 time(s)]

> select #4/B:129@ND2

1 atom, 1 residue, 1 model selected  

> ui tool show "Selection Inspector"

> select intersect #4@@bonds=1

Nothing selected  

> select intersect #4@@bonds=2

Nothing selected  

> ui tool show "Selection Inspector"

> select #4/B:129@ND2

1 atom, 1 residue, 1 model selected  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.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-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3174, in run  
prev_annos = self._process_positional_arguments()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2930, in
_process_positional_arguments  
value, text = self._parse_arg(anno, text, session, False)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2784, in _parse_arg  
value, replacement, rest = annotation.parse(text, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 1486, in parse  
objects = aspec.evaluate(session)  
^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1098, in evaluate  
results = self._left_spec.evaluate(  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1008, in evaluate  
return self.find_matches(session, models, results, ordered,
add_implied=add_implied)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1011, in find_matches  
self._specifier.find_matches(session, models, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 455, in find_matches  
model_spec.find_matches(session, model_list, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 612, in find_matches  
self.my_parts.find_matches(session, model_list, self.sub_parts, results,
ordered,  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 470, in find_matches  
self._check(session, model_list, sub_parts, results, 0, ordered)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 490, in _check  
self._check(session, match_list, sub_parts, results, i + 1, ordered)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 476, in _check  
_add_model_parts(session, model, sub_parts, results, ordered)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 637, in _add_model_parts  
chain_spec.find_selected_parts(model, atoms, num_atoms, my_results)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 572, in find_selected_parts  
subpart.find_selected_parts(model, atoms, num_atoms, sub_results)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 572, in find_selected_parts  
subpart.find_selected_parts(model, atoms, num_atoms, sub_results)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 561, in find_selected_parts  
atoms = self._filter_parts(model, atoms, num_atoms)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 579, in _filter_parts  
mask = model.atomspec_filter(self.Symbol, atoms, num_atoms,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 944, in atomspec_filter  
return self._atomspec_filter_atom(atoms, num_atoms, parts, attrs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1026, in _atomspec_filter_atom  
selected = self._atomspec_attr_filter(atoms, selected, attrs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 979, in _atomspec_attr_filter  
selected = [(selected[i] and choose(obj)) for i, obj in enumerate(objects)]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 979, in <listcomp>  
selected = [(selected[i] and choose(obj)) for i, obj in enumerate(objects)]  
^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 928, in matcher  
return op(v, attr_value)  
^^^^^^^^^^^^^^^^^  
TypeError: '>' not supported between instances of 'list' and 'int'  
  
TypeError: '>' not supported between instances of 'list' and 'int'  
  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 928, in matcher  
return op(v, attr_value)  
^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.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-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3174, in run  
prev_annos = self._process_positional_arguments()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2930, in
_process_positional_arguments  
value, text = self._parse_arg(anno, text, session, False)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2784, in _parse_arg  
value, replacement, rest = annotation.parse(text, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 1486, in parse  
objects = aspec.evaluate(session)  
^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1098, in evaluate  
results = self._left_spec.evaluate(  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1008, in evaluate  
return self.find_matches(session, models, results, ordered,
add_implied=add_implied)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 1011, in find_matches  
self._specifier.find_matches(session, models, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 455, in find_matches  
model_spec.find_matches(session, model_list, results, ordered,
add_implied=add_implied)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 612, in find_matches  
self.my_parts.find_matches(session, model_list, self.sub_parts, results,
ordered,  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 470, in find_matches  
self._check(session, model_list, sub_parts, results, 0, ordered)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 490, in _check  
self._check(session, match_list, sub_parts, results, i + 1, ordered)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 476, in _check  
_add_model_parts(session, model, sub_parts, results, ordered)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 637, in _add_model_parts  
chain_spec.find_selected_parts(model, atoms, num_atoms, my_results)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 572, in find_selected_parts  
subpart.find_selected_parts(model, atoms, num_atoms, sub_results)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 572, in find_selected_parts  
subpart.find_selected_parts(model, atoms, num_atoms, sub_results)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 561, in find_selected_parts  
atoms = self._filter_parts(model, atoms, num_atoms)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 579, in _filter_parts  
mask = model.atomspec_filter(self.Symbol, atoms, num_atoms,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 944, in atomspec_filter  
return self._atomspec_filter_atom(atoms, num_atoms, parts, attrs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1026, in _atomspec_filter_atom  
selected = self._atomspec_attr_filter(atoms, selected, attrs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 979, in _atomspec_attr_filter  
selected = [(selected[i] and choose(obj)) for i, obj in enumerate(objects)]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 979, in <listcomp>  
selected = [(selected[i] and choose(obj)) for i, obj in enumerate(objects)]  
^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 928, in matcher  
return op(v, attr_value)  
^^^^^^^^^^^^^^^^^  
TypeError: '>' not supported between instances of 'list' and 'int'  
  
TypeError: '>' not supported between instances of 'list' and 'int'  
  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/atomspec.py", line 928, in matcher  
return op(v, attr_value)  
^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> select intersect #4@@neighbor>1

Nothing selected  

> select intersect #4@@num_bonds>1

Nothing selected  

> select #4@@num_bonds>1

2045 atoms, 2136 bonds, 388 residues, 1 model selected  

> select #4@@num_bonds=1

814 atoms, 388 residues, 1 model selected  

> select #4@@num_bonds=0

Nothing selected  

> show #4 atoms

> hide #4 cartoons

> select #4/A:132@CZ

1 atom, 1 residue, 1 model selected  

> delete atoms sel

> select #4@@num_bonds=0

2 atoms, 1 residue, 1 model selected  

> delete atoms sel

> save "/Users/sir_mr_dog/Library/CloudStorage/OneDrive-
> UniversityofNebraskaMedicalCenter/Borgstahl Lab/ORNL
> Data/Jun_2026/Reduced/X-ray/phaser_7/dimer_[NAME].pdb" models #3-4

> split #4

Split pruned (#4) into 2 models  
Chain information for pruned A #4.1  
---  
Chain | Description  
A | No description available  
  
Chain information for pruned B #4.2  
---  
Chain | Description  
B | No description available  
  

> save "/Users/sir_mr_dog/Library/CloudStorage/OneDrive-
> UniversityofNebraskaMedicalCenter/Borgstahl Lab/ORNL
> Data/Jun_2026/Reduced/X-ray/phaser_7/[NAME]_monomer.pdb" models #4

> select #4@@bfactor<4.280 | @@bfactor>300.0

Nothing selected  

> select #4@@bfactor<5 | @@bfactor>300.0

4 atoms, 4 residues, 1 model selected  

> select #4@@bfactor<10 | @@bfactor>300.0

220 atoms, 136 bonds, 66 residues, 1 model selected  

> select #4@@bfactor<10 | @@bfactor>50

456 atoms, 280 bonds, 148 residues, 4 models selected  

> show #3 models

> hide #3 models

> show #1 models

> hide #1 models

> show #3 models

> hide sel & #3#4.1 cartoons

> show sel & #3#4.1 atoms

[Repeated 1 time(s)]

> show #!2 models

> show sel & #3#2.1#4.1 atoms

> show #1 models

> show sel atoms

> hide #!4 models

> hide #3 models

> show #3 models

> hide sel & #1,3#2.1 cartoons

[Repeated 1 time(s)]

> hide #!2 models

> hide #1 models

Drag select of 118 atoms, 355 residues, 72 bonds  

> hide sel cartoons

> show sel atoms

> select clear

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> select add #3

3142 atoms, 3234 bonds, 396 residues, 1 model selected  

> show sel atoms

> select clear

> select #4@@bfactor<10 | @@bfactor>50

456 atoms, 280 bonds, 148 residues, 4 models selected  

> hide #3 models

> show #!4 models

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> select clear

> select #4(@@bfactor<10 | @@bfactor>50)

Expected an objects specifier or a keyword  

> select #4 @@bfactor<10 | @@bfactor>50

456 atoms, 280 bonds, 148 residues, 4 models selected  

> select #4 (@@bfactor<10 | @@bfactor>50)

Expected a keyword  

> select #4 [@@bfactor<10 | @@bfactor>50]

Expected a keyword  

> help help:user

> select #4,@@bfactor<10 | @@bfactor>50

Expected an objects specifier or a keyword  

> select #4 (@@bfactor<10 | @@bfactor>50)

Expected a keyword  

> select #4 ((@@bfactor<10) | (@@bfactor>50))

Expected a keyword  

> select #4 ((@@bfactor<10) | (@@bfactor>50))

Expected a keyword  

> select #4((@@bfactor<10) | (@@bfactor>50))

Expected an objects specifier or a keyword  

> select #4((@@bfactor<10) | @CA)

Expected an objects specifier or a keyword  

> select #4(@@bfactor<10 | @CA)

Expected an objects specifier or a keyword  

> select #4 @@bfactor<10 | @CA

1367 atoms, 176 bonds, 1180 residues, 5 models selected  

> select #4 & (@@bfactor<10 | @CA)

575 atoms, 176 bonds, 388 residues, 2 models selected  

> select #4 & @@bfactor<10 | @@bfactor>50

220 atoms, 136 bonds, 66 residues, 1 model selected  

> select clear

> select #4 & @@bfactor<10 | @@bfactor>50

220 atoms, 136 bonds, 66 residues, 1 model selected  

> select #4 @@bfactor<10 | @@bfactor>50

456 atoms, 280 bonds, 148 residues, 4 models selected  

> select #4 & @@bfactor<10 | @@bfactor>50

220 atoms, 136 bonds, 66 residues, 1 model selected  

> select #4&@@bfactor<10 | @@bfactor>50

220 atoms, 136 bonds, 66 residues, 1 model selected  

> save "/Users/sir_mr_dog/Library/CloudStorage/OneDrive-
> UniversityofNebraskaMedicalCenter/Borgstahl Lab/ORNL Data/Jun_2026/selection
> bug demonstration.cxs"

——— End of log from Thu Aug 6 11:56:19 2026 ———

> view name session-start

opened ChimeraX session  

> select #4@@bfactor<10 | @@bfactor>50

453 atoms, 277 bonds, 148 residues, 4 models selected  

> select clear

> select #4&@@bfactor<10 | @@bfactor>50

220 atoms, 136 bonds, 66 residues, 1 model selected  

> ui tool show "Render/Select by Attribute"

> select #4.1@@bfactor<5.0002015902859185 | @@bfactor>40.0

457 atoms, 319 bonds, 143 residues, 5 models selected  

> show #3 models

> hide #!4 models

> show #!4 models

> hide #3 models

> show #3 models

> hide #!4 models

> show #!4 models

> select clear

> select #4&@@bfactor<5.0 | @@bfactor>40.0

13 atoms, 5 bonds, 9 residues, 2 models selected  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M4 Pro
OpenGL vendor: Apple

Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac16,7
      Model Number: Z1FU000A9LL/A
      Chip: Apple M4 Pro
      Total Number of Cores: 14 (10 performance and 4 efficiency)
      Memory: 48 GB
      System Firmware Version: mBoot-18000.120.36
      OS Loader Version: 11881.140.96.701.1

Software:

    System Software Overview:

      System Version: macOS 15.7.7 (24G720)
      Kernel Version: Darwin 24.6.0
      Time since boot: 20 days, 23 hours, 49 minutes

Graphics/Displays:

    Apple M4 Pro:

      Chipset Model: Apple M4 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 20
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    accessible-pygments: 0.0.5
    aiohappyeyeballs: 2.6.2
    aiohttp: 3.13.4
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.13.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.1
    attrs: 26.1.0
    babel: 2.18.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 4.4.3
    bs4: 0.0.2
    build: 1.3.0
    certifi: 2025.7.14
    cftime: 1.6.5
    charset-normalizer: 3.4.7
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.2
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.67.1
    ChimeraX-AtomicLibrary: 14.4
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4.1
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.4
    ChimeraX-Cluster: 1.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.1
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.12
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.2.2
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.8.2
    ChimeraX-Label: 1.5
    ChimeraX-LightingGUI: 1.0
    ChimeraX-ListInfo: 1.3.1
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.3
    ChimeraX-Map: 1.3
    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-MatchAlign: 1.2
    ChimeraX-MatchMaker: 2.4.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.2.0
    ChimeraX-MDcrds: 2.19
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.9
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.23
    ChimeraX-ModelPanel: 1.6.1
    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: 1.0.1
    ChimeraX-MutationScores: 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: 1.15.4
    ChimeraX-OpenFold: 1.0
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.13
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.4
    ChimeraX-ProfileGrids: 1.6
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.8.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.3
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.3.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.12
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.18
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SNFG: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.3
    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: 2.5.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.4
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.50.8
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.6.2
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    click: 8.4.1
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.14.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.2.4
    debugpy: 1.8.21
    decorator: 5.3.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.63.0
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.16.0
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.18
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 2.0.0
    iniconfig: 2.3.0
    ipykernel: 7.1.0
    ipython: 9.9.0
    ipython_pygments_lexers: 1.1.1
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.8.0
    jupyter_core: 5.9.1
    kiwisolver: 1.5.0
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.2
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.1
    narwhals: 2.22.1
    ndindex: 1.10.1
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.14.1
    numpy: 1.26.4
    OpenMM: 8.4.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.7
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.10.0
    plotly: 6.8.0
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.5.2
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.13.4
    pydantic-settings: 2.14.1
    pydantic_core: 2.46.4
    pydata-sphinx-theme: 0.18.0
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.5.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.3.2
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.10.2
    PyQt6-Qt6: 6.10.2
    PyQt6-WebEngine-commercial: 6.10.0
    PyQt6-WebEngine-Qt6: 6.10.2
    PyQt6_sip: 13.10.3
    pytest: 9.0.3
    pytest-cov: 7.1.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.2
    python-multipart: 0.0.32
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.1.0
    rpds-py: 2026.5.1
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.1.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8.4
    Sphinx: 9.0.4
    sphinx-autodoc-typehints: 3.6.1
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    sse-starlette: 3.4.4
    stack-data: 0.6.3
    starlette: 1.3.0
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 3.2.1
    threadpoolctl: 3.6.0
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.7
    tqdm: 4.68.2
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    Unidecode: 1.4.0
    urllib3: 2.7.0
    uvicorn: 0.49.0
    wcwidth: 0.8.1
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    yarl: 1.24.2

[Eric Pettersen]

Hi Miles,

Thanks for reporting this problem. I will try to fix it soon.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[Eric Pettersen]

Fixed it by adding parentheses to the command, which makes it clearer anyway. Fix will be in tomorrow's daily build.

Fix: ​https://github.com/RBVI/ChimeraX/commit/7f673b86a5c0cf7f271e3a59af8df0e3f391f61f