No Contacts output

[schell.a@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
I can't get any results from Structure Analysis>Contacts between nicotine and its receptor. I'm following a tutorial for class and doing the same thing as others but getting different results. I've attached an image showing the parameters I set to show contacts and my results from the log are below.

contacts sel ignoreHiddenModels true reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True

0 contacts
atom1  atom2  overlap  distance
No contacts

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6CNJ

Summary of feedback from opening 6CNJ fetched from pdb  
---  
notes | Fetching compressed mmCIF 6cnj from http://files.rcsb.org/download/6cnj.cif  
Fetching CCD BMA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/BMA/BMA.cif  
Fetching CCD NA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/NA/NA.cif  
Fetching CCD NAG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NAG/NAG.cif  
Fetching CCD NCT from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/T/NCT/NCT.cif  
Fetching CCD Y01 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/1/Y01/Y01.cif  
  
6cnj title:  
Structure of the 2alpha3beta stiochiometry of the human Alpha4Beta2 nicotinic
receptor [more info...]  
  
Chain information for 6cnj #1  
---  
Chain | Description | UniProt  
A D | Neuronal acetylcholine receptor subunit alpha-4 | ACHA4_HUMAN 1-338 345-386  
B C E | Neuronal acetylcholine receptor subunit beta-2 | ACHB2_HUMAN 1-328 337-393  
F H J | IgG1 Kappa Light Chain |   
G I K | IgG1 Heavy Chain |   
  
Non-standard residues in 6cnj #1  
---  
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)  
NA — sodium ion  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
NCT — (S)-3-(1-methylpyrrolidin-2-yl)pyridine ((S)-(-)-nicotine;
3-[(2S)-1-methyl-2-pyrrolidinyl] pyridine)  
Y01 — cholesterol hemisuccinate  
  

> hide #!1 models

> show #!1 models

Drag select of 24917 atoms, 5 pseudobonds, 492 bonds  
Drag select of 25343 atoms, 5 pseudobonds, 492 bonds  

> select clear

> select

25343 atoms, 26068 bonds, 5 pseudobonds, 3146 residues, 2 models selected  

> select clear

> select add #1

25343 atoms, 26068 bonds, 5 pseudobonds, 3146 residues, 2 models selected  

> select subtract #1

Nothing selected  

> sequence chain #1/A#1/D

Alignment identifier is 1  

> select /A:5-381

3049 atoms, 3137 bonds, 1 pseudobond, 370 residues, 2 models selected  

> select /D:5-381

3049 atoms, 3137 bonds, 1 pseudobond, 370 residues, 2 models selected  

> select add #1

25343 atoms, 26068 bonds, 5 pseudobonds, 3146 residues, 2 models selected  

> select subtract #1

Nothing selected  

> select /B:16@NE

1 atom, 1 residue, 1 model selected  

> select clear

> select /B:7@CA

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

86 atoms, 86 bonds, 10 residues, 1 model selected  

> select up

2641 atoms, 2712 bonds, 325 residues, 1 model selected  

> select clear

> select add #1

25343 atoms, 26068 bonds, 5 pseudobonds, 3146 residues, 2 models selected  

> hide (#!1 & sel) target a

> show sel cartoons

> select clear

> select /G/I/K

4959 atoms, 5100 bonds, 654 residues, 1 model selected  

> hide sel cartoons

> select /F/H/J

5085 atoms, 5211 bonds, 654 residues, 1 model selected  

> hide sel cartoons

> save C:/Users/annas/Documents/modeling_step_12.png width 699 height 523
> supersample 3

> select /A

3132 atoms, 3227 bonds, 1 pseudobond, 375 residues, 2 models selected  

> color (#!1 & sel) lime

> ui tool show "Side View"

> select up

25343 atoms, 26068 bonds, 5 pseudobonds, 3146 residues, 2 models selected  

> select down

3132 atoms, 3227 bonds, 1 pseudobond, 375 residues, 2 models selected  

> ui mousemode right translate

> ui mousemode right "move picked models"

> ui mousemode right "translate selected models"

> ui mousemode right "move picked models"

> ui mousemode right select

> ui mousemode right "move picked models"

> movie record

> turn y 2 180

> wait 180

> movie encode C:\ProgramData\ChimeraX\movie1.mp4

Movie saved to C:\ProgramData\ChimeraX\movie1.mp4  
  

> ui tool show "Show Sequence Viewer"

> sequence chain /A /D

Alignment identifier is 2  

> select clear

[Repeated 1 time(s)]

> select /A,D:6-19,75-79,217-241,247-270,278-307,315-330,343-378

2474 atoms, 2522 bonds, 300 residues, 1 model selected  

> select clear

> hide #!1 target m

[Repeated 1 time(s)]

> show #!1 models

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> select clear

[Repeated 6 time(s)]

> select /A:381

14 atoms, 15 bonds, 1 residue, 1 model selected  

> select clear

> select /A:106-381

2207 atoms, 2273 bonds, 1 pseudobond, 269 residues, 2 models selected  

> select clear

> select /A:36-381

2794 atoms, 2876 bonds, 1 pseudobond, 339 residues, 2 models selected  

> select clear

> select /A:5-321

2596 atoms, 2670 bonds, 317 residues, 1 model selected  

> select clear

> select /A:5-247

2003 atoms, 2063 bonds, 243 residues, 1 model selected  

> select clear

> select /A:5-381

3049 atoms, 3137 bonds, 1 pseudobond, 370 residues, 2 models selected  

> color (#!1 & sel) blue

> select ~sel & ##selected

22294 atoms, 22931 bonds, 4 pseudobonds, 2776 residues, 2 models selected  

> hide sel atoms

> hide sel cartoons

> select /B

2973 atoms, 3059 bonds, 1 pseudobond, 360 residues, 2 models selected  

> color (#!1 & sel) purple

> select /A:5-381

3049 atoms, 3137 bonds, 1 pseudobond, 370 residues, 2 models selected  

> show sel cartoons

[Repeated 1 time(s)]

> color (#!1 & sel) orange

> color (#!1 & sel) blue

> select clear

> show cartoons

> undo

> show target ab

> undo

> select /A/D

6263 atoms, 6454 bonds, 2 pseudobonds, 749 residues, 2 models selected  

> show sel cartoons

> select /B/C/E

8919 atoms, 9177 bonds, 3 pseudobonds, 1080 residues, 2 models selected  

> show sel cartoons

> select helix

5996 atoms, 6107 bonds, 741 residues, 1 model selected  

> select helix

5996 atoms, 6107 bonds, 741 residues, 1 model selected  

> color sel orange

> undo

> select /A

3132 atoms, 3227 bonds, 1 pseudobond, 375 residues, 2 models selected  

> select helix

5996 atoms, 6107 bonds, 741 residues, 1 model selected  

> undo

> color (#!1 & sel) byelement

> select /A:5

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

> select /A:5-148

1194 atoms, 1229 bonds, 144 residues, 1 model selected  

> undo

> select helix

5996 atoms, 6107 bonds, 741 residues, 1 model selected  

> select down

5996 atoms, 6107 bonds, 741 residues, 1 model selected  

> color sel orange

> undo

> select /B

2973 atoms, 3059 bonds, 1 pseudobond, 360 residues, 2 models selected  

> select
> /A:36-51,56-68,85-88,97-99,114-117,122-125,128-133,146-155,163-167,183-195,204-215

745 atoms, 754 bonds, 90 residues, 1 model selected  

> select /A:6-19,75-79,217-222,224-235,237-241,247-267,278-306,315-330,343-377

1178 atoms, 1200 bonds, 143 residues, 1 model selected  

> color sel orange

> select
> /A:36-51,56-68,85-88,97-99,114-117,122-125,128-133,146-155,163-167,183-195,204-215

745 atoms, 754 bonds, 90 residues, 1 model selected  

> color sel cyan

> select sequence CC

24 atoms, 24 bonds, 4 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> select /A:199

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

> select /A:199-200

12 atoms, 12 bonds, 2 residues, 1 model selected  

> show sel atoms

> select /A:196

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

> select /A:196-203

64 atoms, 65 bonds, 8 residues, 1 model selected  

> color sel hot pink

> select clear

Drag select of 10 residues  

> select clear

> select /A

3132 atoms, 3227 bonds, 1 pseudobond, 375 residues, 2 models selected  

> select /A:199

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

> select /A:199-200

12 atoms, 12 bonds, 2 residues, 1 model selected  

> color sel yellow

> view sel

> style sel stick

Changed 12 atom styles  

> style sel sphere

Changed 12 atom styles  

> style sel ball

Changed 12 atom styles  

> style sel stick

Changed 12 atom styles  

> label sel text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> ui mousemode right "move picked models"

> ui mousemode right select

Drag select of 1 residues  

> undo

> ui mousemode right "move label"

> select sequence CSIDVTFFPFDQQN

232 atoms, 238 bonds, 28 residues, 1 model selected  

> show sel cartoons

> ui mousemode right rotate

> select clear

> lighting simple

> undo

> view sel

> ui mousemode right "move picked models"

> ui mousemode right rotate

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.65793,-0.75285,0.018454,142.19,0.74993,0.65722,0.075237,-64.971,-0.068771,-0.035661,0.99699,14.264

> select sequence CSIDVTFFPFDQQN

232 atoms, 238 bonds, 28 residues, 1 model selected  

> select /A:135

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

> select /A:135-148

116 atoms, 119 bonds, 14 residues, 1 model selected  

> select /A:135

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

> select /A:135-149

122 atoms, 126 bonds, 15 residues, 1 model selected  

> show sel cartoons

> color sel red

> select /A:135-149

122 atoms, 126 bonds, 15 residues, 1 model selected  

> select /A:135-149

122 atoms, 126 bonds, 15 residues, 1 model selected  

> select /A:135

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

> select /A:135

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

> select /A:135

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

> select /A:135-149

122 atoms, 126 bonds, 15 residues, 1 model selected  

> select /A:135-149

122 atoms, 126 bonds, 15 residues, 1 model selected  

> select
> /A:36-51,56-68,85-88,97-99,114-117,122-125,128-133,146-155,163-167,183-195,204-215

745 atoms, 754 bonds, 90 residues, 1 model selected  

> select /A:135-149

122 atoms, 126 bonds, 15 residues, 1 model selected  

> select /A:135

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

> select /A:135-149

122 atoms, 126 bonds, 15 residues, 1 model selected  

> select /A:6-19,75-79,217-222,224-235,237-241,247-267,278-306,315-330,343-377

1178 atoms, 1200 bonds, 143 residues, 1 model selected  

> select
> /A:6-19,75-79,135,217-222,224-235,237-241,247-267,278-306,315-330,343-377

1184 atoms, 1205 bonds, 144 residues, 1 model selected  

> select
> /A:6-19,75-79,135,217-222,224-235,237-241,247-267,278-306,315-330,343-377

1184 atoms, 1205 bonds, 144 residues, 1 model selected  

> select
> /A:6-19,75-79,135,217-222,224-235,237-241,247-267,278-306,315-330,343-377

1184 atoms, 1205 bonds, 144 residues, 1 model selected  

> select
> /A:6-19,75-79,135,217-222,224-235,237-241,247-267,278-306,315-330,343-377

1184 atoms, 1205 bonds, 144 residues, 1 model selected  

> select /A:135-149

122 atoms, 126 bonds, 15 residues, 1 model selected  

> select /A:135-149

122 atoms, 126 bonds, 15 residues, 1 model selected  

> select /A:135-149

122 atoms, 126 bonds, 15 residues, 1 model selected  

> select clear

> select /A:135-149

122 atoms, 126 bonds, 15 residues, 1 model selected  

> select /A:135-149

122 atoms, 126 bonds, 15 residues, 1 model selected  

> select /A:135

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

> select /A:135

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

> select /A:135

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

> select /A:135,149

12 atoms, 11 bonds, 2 residues, 1 model selected  

> color sel yellow

> show sel atoms

> style sel stick

Changed 12 atom styles  

> style sel sphere

Changed 12 atom styles  

> view sel

[Repeated 1 time(s)]

> undo

[Repeated 1 time(s)]

> style sel stick

Changed 12 atom styles  

> label sel text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> view sel

> ui mousemode right "move label"

> ui mousemode right select

> select clear

> view

> ui mousemode right rotate

> ui mousemode right zoom

> ui mousemode right "move picked models"

> save C:/Users/annas/Modeling_Step_23.png width 699 height 523 supersample 3

> select ::name="NCT"

24 atoms, 26 bonds, 2 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> show sel atoms

> color sel white

> style sel stick

Changed 24 atom styles  

> color sel byhetero

> view matrix models
> #1,0.65793,-0.75285,0.018454,135.05,0.74993,0.65722,0.075237,-72.475,-0.068771,-0.035661,0.99699,15.121

> view matrix models
> #1,0.65793,-0.75285,0.018454,133.6,0.74993,0.65722,0.075237,-83.878,-0.068771,-0.035661,0.99699,15.067

> style sel ball

Changed 24 atom styles  

> select /B

2973 atoms, 3059 bonds, 1 pseudobond, 360 residues, 2 models selected  

> view matrix models
> #1,0.65793,-0.75285,0.018454,122.45,0.74993,0.65722,0.075237,-94.063,-0.068771,-0.035661,0.99699,15.709

> select clear

> select /A:402@C2

1 atom, 1 residue, 1 model selected  

> select up

12 atoms, 13 bonds, 1 residue, 1 model selected  

> select sel :< 5 & ~sel

123 atoms, 122 bonds, 13 residues, 1 model selected  

> show sel atoms

> name frozen binding_site sel

> style sel stick

Changed 123 atom styles  

> select /A:402@C2

1 atom, 1 residue, 1 model selected  

> select up

12 atoms, 13 bonds, 1 residue, 1 model selected  

> ui tool show Contacts

> contacts sel ignoreHiddenModels true color #99ff6a reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: True
    
    0 contacts
    atom1  atom2  overlap  distance
    

  
No contacts  

> select up

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

> select up

12 atoms, 13 bonds, 1 residue, 1 model selected  

> ui tool show Contacts

> contacts sel ignoreHiddenModels true color #99ff6a reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: True
    
    0 contacts
    atom1  atom2  overlap  distance
    

  
No contacts  

> select up

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

> select up

12 atoms, 13 bonds, 1 residue, 1 model selected  

> select up

3132 atoms, 3227 bonds, 375 residues, 1 model selected  

> select down

12 atoms, 13 bonds, 1 residue, 1 model selected  

> ui tool show Contacts

> contacts sel ignoreHiddenModels true color #00ff7f reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: True
    
    0 contacts
    atom1  atom2  overlap  distance
    

  
No contacts  

> ui tool show Contacts

> contacts sel ignoreHiddenModels true select true reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: True
    
    0 contacts
    atom1  atom2  overlap  distance
    

  
No contacts  

> select binding_site

123 atoms, 122 bonds, 13 residues, 1 model selected  

> select up

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

> select up

12 atoms, 13 bonds, 1 residue, 1 model selected  

> undo

[Repeated 2 time(s)]

> ui tool show Contacts

> contacts sel ignoreHiddenModels true select true reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: True
    
    0 contacts
    atom1  atom2  overlap  distance
    

  
No contacts  

> select /A:402@C2

1 atom, 1 residue, 1 model selected  

> select up

12 atoms, 13 bonds, 1 residue, 1 model selected  

> select sel :< 5 & ~sel

123 atoms, 122 bonds, 13 residues, 1 model selected  

> undo

> select sel :< 5 & ~sel

123 atoms, 122 bonds, 13 residues, 1 model selected  

> select binding_site

123 atoms, 122 bonds, 13 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 123 atom styles  

> style sel sphere

Changed 123 atom styles  

> style sel stick

Changed 123 atom styles  

> select /A:402@N2

1 atom, 1 residue, 1 model selected  

> select up

12 atoms, 13 bonds, 1 residue, 1 model selected  

> select up

3132 atoms, 3227 bonds, 375 residues, 1 model selected  

> select down

12 atoms, 13 bonds, 1 residue, 1 model selected  

> ui tool show Contacts

> contacts sel ignoreHiddenModels true select true reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: True
    
    0 contacts
    atom1  atom2  overlap  distance
    

  
No contacts  

> undo

[Repeated 3 time(s)]

> select add /A:402@C6

124 atoms, 122 bonds, 14 residues, 1 model selected  

> select up

135 atoms, 135 bonds, 14 residues, 1 model selected  

> ui tool show Contacts

> contacts sel ignoreHiddenModels true select true reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: True
    
    0 contacts
    atom1  atom2  overlap  distance
    

  
No contacts  

> select /A:402@C6

1 atom, 1 residue, 1 model selected  

> select up

12 atoms, 13 bonds, 1 residue, 1 model selected  

> ui tool show Clashes

> clashes sel ignoreHiddenModels true

No clashes  

> ui tool show Contacts

> contacts sel ignoreHiddenModels true select true reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: True
    
    0 contacts
    atom1  atom2  overlap  distance
    

  
No contacts  

> ui tool show Contacts

> contacts sel ignoreHiddenModels true reveal true log true

No atoms match given atom specifier  

> select up

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

> select up

12 atoms, 13 bonds, 1 residue, 1 model selected  

> ui tool show Contacts

> view matrix models
> #1,0.65793,-0.75285,0.018454,136.24,0.74993,0.65722,0.075237,-68.004,-0.068771,-0.035661,0.99699,15.099

> view matrix models
> #1,0.65793,-0.75285,0.018454,153.67,0.74993,0.65722,0.075237,-65.341,-0.068771,-0.035661,0.99699,13.915

> select up

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

> select up

12 atoms, 13 bonds, 1 residue, 1 model selected  

> contacts sel ignoreHiddenModels true reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: True
    
    0 contacts
    atom1  atom2  overlap  distance
    

  
No contacts  

> select clear

> view matrix models
> #1,0.65793,-0.75285,0.018454,152.96,0.74993,0.65722,0.075237,-65.58,-0.068771,-0.035661,0.99699,14.16

> ui mousemode right zoom

> ui mousemode right "move picked models"

> view matrix models
> #1,0.65793,-0.75285,0.018454,154.17,0.74993,0.65722,0.075237,-50.852,-0.068771,-0.035661,0.99699,-16.606

> ui mousemode right "rotate selected models"

> ui mousemode right "move picked models"

> select /A:402@C2

1 atom, 1 residue, 1 model selected  

> select up

12 atoms, 13 bonds, 1 residue, 1 model selected  

> ui tool show Contacts

> contacts sel ignoreHiddenModels true reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: True
    
    0 contacts
    atom1  atom2  overlap  distance
    

  
No contacts  

> ui tool show Contacts

> contacts sel ignoreHiddenModels true reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: True
    
    0 contacts
    atom1  atom2  overlap  distance
    

  
No contacts  

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.98097,0.12979,-0.14442,278.36,-0.12572,-0.99137,-0.037021,298.09,-0.14798,-0.01816,0.98882,-7.2515

> ui mousemode right "move picked models"

> undo

> view matrix models
> #1,0.65793,-0.75285,0.018454,150.77,0.74993,0.65722,0.075237,-50.968,-0.068771,-0.035661,0.99699,-19.66

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.50626,-0.61935,-0.60009,237.28,0.79184,0.60948,0.038986,-45.348,0.3416,-0.49492,0.79898,12.995

> view matrix models
> #1,0.62983,-0.52921,-0.56855,204.67,0.71355,0.6834,0.15435,-60.295,0.30686,-0.5029,0.80804,17.445

> ui mousemode right rotate

> ui mousemode right "move picked models"

> view matrix models
> #1,0.62983,-0.52921,-0.56855,213.41,0.71355,0.6834,0.15435,-58.428,0.30686,-0.5029,0.80804,23.069

> view matrix models
> #1,0.62983,-0.52921,-0.56855,203.87,0.71355,0.6834,0.15435,-60.488,0.30686,-0.5029,0.80804,16.934

> view matrix models
> #1,0.62983,-0.52921,-0.56855,203.83,0.71355,0.6834,0.15435,-63.554,0.30686,-0.5029,0.80804,17.315

> select binding_site

123 atoms, 122 bonds, 13 residues, 1 model selected  

> select add /A:402@C2

124 atoms, 121 bonds, 14 residues, 1 model selected  

> select up

135 atoms, 135 bonds, 14 residues, 1 model selected  

> cartoon sel

> ui tool show Contacts

> contacts sel ignoreHiddenModels true reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: True
    
    0 contacts
    atom1  atom2  overlap  distance
    

  
No contacts  

> save C:/Users/annas/Documents/Step28.cxs

> select /A:402@C3

1 atom, 1 residue, 1 model selected  

> select /A:402@C3

1 atom, 1 residue, 1 model selected  

> select up

12 atoms, 13 bonds, 1 residue, 1 model selected  

> ui tool show Contacts

> contacts sel ignoreHiddenModels true reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: True
    
    0 contacts
    atom1  atom2  overlap  distance
    

  
No contacts  

> contacts sel ignoreHiddenModels true reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: True
    
    0 contacts
    atom1  atom2  overlap  distance
    

  
No contacts  

> select binding_site

123 atoms, 122 bonds, 13 residues, 1 model selected  

> ui tool show "Selection Inspector"

> select /A:402@C3

1 atom, 1 residue, 1 model selected  

> select up

12 atoms, 13 bonds, 1 residue, 1 model selected  

> select sel :< 5 & ~sel

123 atoms, 122 bonds, 13 residues, 1 model selected  

> show sel atoms

> name frozen binding_site_2 sel

> undo

> view matrix models
> #1,0.62983,-0.52921,-0.56855,193.14,0.71355,0.6834,0.15435,-60.684,0.30686,-0.5029,0.80804,15.215

> view matrix models
> #1,0.62983,-0.52921,-0.56855,192.98,0.71355,0.6834,0.15435,-66.014,0.30686,-0.5029,0.80804,19.063

> select /A:402@C3

1 atom, 1 residue, 1 model selected  

> select up

12 atoms, 13 bonds, 1 residue, 1 model selected  

> ui tool show Contacts

> contacts sel ignoreHiddenModels true reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: True
    
    0 contacts
    atom1  atom2  overlap  distance
    

  
No contacts  

> select binding_site_2

123 atoms, 122 bonds, 13 residues, 1 model selected  

> label sel text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> save C:/Users/annas/Documents/labeled_all.png width 699 height 523
> supersample 3

> select /B:79

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

> select /B:79

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

> select /B:112

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

> select /B:80

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

> ~label sel residues

[Repeated 2 time(s)]

> select /B:111@CB

1 atom, 1 residue, 1 model selected  

> ~label sel residues

[Repeated 4 time(s)]

> select up

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

> select down

1 bond, 1 model selected  

> select up

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

> select up

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

> ~label sel residues

> select up

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

> select up

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

> ~label sel residues

> select up

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

> ~label sel residues

> view matrix models
> #1,0.62983,-0.52921,-0.56855,184.26,0.71355,0.6834,0.15435,-66.42,0.30686,-0.5029,0.80804,16.185

> select up

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

> ~label sel residues

> select /A:204@CG

1 atom, 1 residue, 1 model selected  

> select up

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

> ~label sel residues

> view matrix models
> #1,0.62983,-0.52921,-0.56855,188.8,0.71355,0.6834,0.15435,-64.825,0.30686,-0.5029,0.80804,17.985

> select /B:108

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

> select up

124 atoms, 127 bonds, 15 residues, 1 model selected  

> select down

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

> ~label sel residues

> select /B:271

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

> select up

226 atoms, 231 bonds, 29 residues, 1 model selected  

> select up

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

> ~label sel residues

> select up

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

> ~label sel residues

> select /B:57@CG

1 atom, 1 residue, 1 model selected  

> select up

14 atoms, 15 bonds, 1 residue, 1 model selected  

> ~label sel residues

> select up

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

> ~label sel residues

> select /A:134

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

> select /A:271

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

> select A:135

Expected an objects specifier or a keyword  

> select /A:135

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

> view matrix models
> #1,0.62983,-0.52921,-0.56855,192.59,0.71355,0.6834,0.15435,-57.706,0.30686,-0.5029,0.80804,20.751

> view matrix models
> #1,0.62983,-0.52921,-0.56855,195.87,0.71355,0.6834,0.15435,-61.024,0.30686,-0.5029,0.80804,21.074

> save C:/Users/annas/Documents/modeling_step_29.png width 699 height 523
> supersample 3

> view matrix models
> #1,0.62983,-0.52921,-0.56855,206.12,0.71355,0.6834,0.15435,-59.276,0.30686,-0.5029,0.80804,20.933

> select /D:402@C8

1 atom, 1 residue, 1 model selected  

> select up

12 atoms, 13 bonds, 1 residue, 1 model selected  

> ui tool show Contacts

> contacts sel ignoreHiddenModels true reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: True
    
    0 contacts
    atom1  atom2  overlap  distance
    

  
No contacts  




OpenGL version: 3.3.0 Core Profile Context 23.19.12.03.240603
OpenGL renderer: AMD Radeon (TM) Graphics
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: LENOVO
Model: 83B2
OS: Microsoft Windows 11 Home (Build 22631)
Memory: 6,287,323,136
MaxProcessMemory: 137,438,953,344
CPU: 12 AMD Ryzen 5 7530U with Radeon Graphics         
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    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-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-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: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    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-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.5
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pywin32: 306
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    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
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    WMI: 1.5.1
File attachment: Screenshot 2025-01-24 223149.png

Screenshot 2025-01-24 223149.png​

[schell.a@…]

Added by email2trac

[pett]

Reported by Anna Schell

[pett]

Hi Anna,

Thanks for reporting this problem. I can reproduce it, and I will let you know (via this ticket) when there is a fix.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[pett]

Script that reproduces the issue. The "view matrix" command is needed, otherwise things work.

[pett]

Fixed. Fix in the next daily build. Again, thanks for reporting the problem!

Fix: ​https://github.com/RBVI/ChimeraX/commit/979d00ef73da7b9d669fa584c1c269528b9b52d3