kvfinder: self._positions is None

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-6.14.1-061401-generic-x86_64-with-glibc2.39
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open1fno

Unknown command: open1fno  

> open1fmo

Unknown command: open1fmo  

> open 1fmo

Summary of feedback from opening 1fmo fetched from pdb  
---  
notes | Fetching compressed mmCIF 1fmo from http://files.rcsb.org/download/1fmo.cif  
Fetching CCD ADN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ADN/ADN.cif  
  
1fmo title:  
Crystal structure of A polyhistidine-tagged recombinant catalytic subunit of
camp-dependent protein kinase complexed with the peptide inhibitor pki(5-24)
and adenosine [more info...]  
  
Chain information for 1fmo #1  
---  
Chain | Description | UniProt  
E | CAMP-DEPENDENT PROTEIN KINASE | KAPCA_MOUSE 1-350  
I | HEAT STABLE RABBIT SKELETAL MUSCLE INHIBITOR PROTEIN | IPKA_RABIT 5-24  
  
Non-standard residues in 1fmo #1  
---  
ADN — adenosine  
  

> hide #1 models

> show #1 models

> undo

> redo

> select add #1

3058 atoms, 3043 bonds, 449 residues, 1 model selected  

> save /home/taysa.bassani/1FMO.pdb relModel #1

> select #1

3058 atoms, 3043 bonds, 449 residues, 1 model selected  

> select #1/i

164 atoms, 159 bonds, 27 residues, 1 model selected  

> select #1/i:18

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

> select #1/i:18@ca

1 atom, 1 residue, 1 model selected  

> select /I:18

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

> select /E:316

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

> select /E:77

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

> select /E:230

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

> select /E:235

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

> select /E:129

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

> select /E:133

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

> select /E:77

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

> select /E:49

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

> select /E:240

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

> select /E:202

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

> select clear

> select O

632 atoms, 449 residues, 1 model selected  

> select C

1912 atoms, 1564 bonds, 359 residues, 1 model selected  

> select /E

2894 atoms, 2884 bonds, 422 residues, 1 model selected  

> select /I

164 atoms, 159 bonds, 27 residues, 1 model selected  

> select ::name="ADN"::name="HOH"

109 atoms, 21 bonds, 91 residues, 1 model selected  

> select sequence At

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

> select @@bfactor>=90.36553300733495 & @@bfactor<=99.4682078239609

54 atoms, 48 residues, 1 model selected  

> select clear

Drag select of 51 residues  
Drag select of 33 residues  

> select clear

Drag select of 58 residues  

> select up

937 atoms, 950 bonds, 113 residues, 1 model selected  

> select up

2792 atoms, 2863 bonds, 338 residues, 1 model selected  

> select up

2894 atoms, 2884 bonds, 422 residues, 1 model selected  

> select down

2792 atoms, 2863 bonds, 338 residues, 1 model selected  

> select down

937 atoms, 950 bonds, 113 residues, 1 model selected  

> select down

498 atoms, 58 residues, 1 model selected  

> select down

498 atoms, 58 residues, 1 model selected  

> select up

937 atoms, 950 bonds, 113 residues, 1 model selected  

> select up

2792 atoms, 2863 bonds, 338 residues, 1 model selected  

> select up

2894 atoms, 2884 bonds, 422 residues, 1 model selected  

> select up

3058 atoms, 3043 bonds, 449 residues, 1 model selected  

> select up

3058 atoms, 3043 bonds, 449 residues, 1 model selected  

> select down

2894 atoms, 2884 bonds, 422 residues, 1 model selected  

> select down

2792 atoms, 2863 bonds, 338 residues, 1 model selected  

> select down

937 atoms, 950 bonds, 113 residues, 1 model selected  

> select down

498 atoms, 58 residues, 1 model selected  

> select down

498 atoms, 58 residues, 1 model selected  

> select sel @< 5

751 atoms, 710 bonds, 127 residues, 1 model selected  

> show sel target ab

[Repeated 1 time(s)]

> select sel @< 5

1052 atoms, 995 bonds, 179 residues, 1 model selected  

> select clear

> hide target a

> show target ab

> style sphere

Changed 3058 atom styles  

> style stick

Changed 3058 atom styles  

> hide #* target a

> show target ab

> surface

> surface style mesh

> surface style dot

> surface style solid

> transparency 80

> transparency 40

> surface hidePatches

> hide target a

> color yellow

> color byhetero

[Repeated 1 time(s)]

> color blue

> ui tool show "Color Actions"

> color magenta

> set bgColor white

No target buttons for the coloring action are checked  
[Repeated 2 time(s)]

> label #1 attribute label_one_letter_code

> hide #1.3 models

> show #1.3 models

> hide #1.3 models

> show #1.3 models

> view

> cofr frontCenter

> ui tool show "Color Actions"

> set bgColor black

Cannot color background by polymer  
No target buttons for the coloring action are checked  

> color blue target a

> hide #1.3 models

> color #1.1-2#!1 red

> cartoon #1.1-2#!1

> show #1.1-2#!1 target ab

> hide #1.1-2#!1 target a

> label #1.1-2#!1 atoms attribute name

> ui tool show "Side View"

> ui tool show "Show Sequence Viewer"

> sequence chain /E

Alignment identifier is 1/E  

> select /E:333

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

> select /E:333-350

155 atoms, 156 bonds, 18 residues, 1 model selected  

> select /E:301

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

> select /E:301-350

423 atoms, 434 bonds, 50 residues, 1 model selected  

> open 5h3q

Summary of feedback from opening 5h3q fetched from pdb  
---  
notes | Fetching compressed mmCIF 5h3q from http://files.rcsb.org/download/5h3q.cif  
Fetching CCD 7HF from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/F/7HF/7HF.cif  
Fetching CCD DTT from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/T/DTT/DTT.cif  
Fetching CCD NA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/NA/NA.cif  
  
5h3q title:  
Crystal Structure of TrkA kinase with ligand [more info...]  
  
Chain information for 5h3q #2  
---  
Chain | Description | UniProt  
A | High affinity nerve growth factor receptor | NTRK1_HUMAN 473-796  
  
Non-standard residues in 5h3q #2  
---  
7HF —
1-[(3S,4R)-4-[3,4-bis(fluoranyl)phenyl]-1-(2-methoxyethyl)pyrrolidin-3-yl]-3-(5-ethoxy-4-methyl-2-phenyl-
pyrazol-3-yl)urea  
DTT — 2,3-dihydroxy-1,4-dithiobutane (1,4-dithiothreitol)  
NA — sodium ion  
  
16 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A

Alignment identifier is 2/A  

> sequence align #1/E#2/A

Alignment identifier is 1  
Associated 1fmo chain E to chain E with 0 mismatches  
Associated 5h3q chain A to chain A with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: HV55IXF1WALF7VSQ  
Webservices job finished: HV55IXF1WALF7VSQ  

> viwe:ADN

Unknown command: viwe:ADN  

> close #2

> view :ADN

No displayed objects specified.  

> select ligand

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

> color sel yellow

> select

3058 atoms, 3043 bonds, 449 residues, 2 models selected  

> show (#!1 & sel) target ab

> view :ADN

> select /E:351@O3'

1 atom, 1 residue, 1 model selected  

> select add /E:351@O3'

1 atom, 1 bond, 1 residue, 1 model selected  

> ui tool show Distances

Exactly two atoms must be selected!  

> select add /E:351@O3'

1 atom, 1 bond, 1 residue, 1 model selected  
Exactly two atoms must be selected!  

> select /E:127@OE2

1 atom, 1 residue, 1 model selected  

> select add /E:351@O3'

2 atoms, 2 residues, 2 models selected  

> distance /E:127@OE2 /E:351@O3'

Distance between /E GLU 127 OE2 and ADN 351 O3': 3.086Å  

> select add /E:351@O2'

3 atoms, 2 residues, 2 models selected  
Exactly two atoms must be selected!  

> select /E:127@OE2

1 atom, 1 residue, 1 model selected  

> select add /E:351@O2'

2 atoms, 2 residues, 2 models selected  

> distance /E:127@OE2 /E:351@O2'

Distance between /E GLU 127 OE2 and ADN 351 O2': 2.337Å  

> ui tool show "Render/Select by Attribute"

> color byattribute a:bfactor #!1 target cabs palette
> 1,blue:50.5,white:100,red

3058 atoms, 449 residues, 2 surfaces, atom bfactor range 1 to 100  

> key blue-white-red :1 :51 :100 showTool true

> ui mousemode right "color key"

> ui mousemode right "move label"

> 2Dlabels text 2b-factor

Unknown command: 2Dlabels text 2b-factor  

> 2dlabels text 2b-factor

> ui mousemode right "move label"

> color byattribute a:bfactor #!1 target cabs palette
> 1,blue:50.5,white:100,red

3058 atoms, 449 residues, 2 surfaces, atom bfactor range 1 to 100  

> ui tool show "Add Hydrogens"

> ui tool show "Change Chain IDs"

> changechains sel E A

Cannot reassign chain ID to only part of polymeric chain (/E)  

> changechains sel I B

No residues specified have any of the 'from' chain IDs  

> ui tool show "Change Chain IDs"

[Repeated 1 time(s)]

> select add #1.2

159 atoms, 22 residues, 2 models selected  

> select subtract #1.1

158 atoms, 21 residues, 3 models selected  

> select subtract #1.2

1 atom, 1 residue, 2 models selected  

> select add #1.1

2793 atoms, 339 residues, 1 model selected  

> select add #1.2

2950 atoms, 359 residues, 2 models selected  

> ui tool show "Renumber Residues"

> renumber /E:13-350 seqStart 10

Proposed renumbering conflicts with existing residue /E ADN 351  

> toolshed show

> preset "initial styles" sticks

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

> preset "initial styles" cartoon

Using preset: Initial Styles / Cartoon  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset cartoons/nucleotides cylinders/stubs

Using preset: Cartoons/Nucleotides / Cylinders/Stubs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> preset cartoons/nucleotides licorice/ovals

Using preset: Cartoons/Nucleotides / Licorice/Ovals  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh default arrows f x round width 1 thick 1
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides tube/slab shape ellipsoid

  

> preset "initial styles" cartoon

Using preset: Initial Styles / Cartoon  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> preset "overall look" "publication 2 (depth-cued)"

Using preset: Overall Look / Publication 2 (Depth-Cued)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes f
    lighting depthCue t

  

> preset "molecular surfaces" "ghostly white"

Using preset: Molecular Surfaces / Ghostly White  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> preset "initial styles" sticks

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

> preset "initial styles" cartoon

Using preset: Initial Styles / Cartoon  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> surface (#!1 & sel)

> ui tool show "Color Key"

> ui mousemode right "color key"

> key blue-white-red :1 :51 :100

> hide #4.1 models

> show #4.1 models

> hide #4.1 models

> hide #2.1 models

> show #2.1 models

> hide #3 models

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> color (#!1 & sel) red

> color (#!1 & sel) light gray

> surface hidePatches (#!1 & sel)

> ui tool show "Color Actions"

> set bgColor black

> hide #4.1 models

> graphics silhouettes false

> graphics silhouettes true

> preset "initial styles" sticks

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

> preset "initial styles" cartoon

Using preset: Initial Styles / Cartoon  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset cartoons/nucleotides licorice/ovals

Using preset: Cartoons/Nucleotides / Licorice/Ovals  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh default arrows f x round width 1 thick 1
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides tube/slab shape ellipsoid

  

> preset cartoons/nucleotides cylinders/stubs

Using preset: Cartoons/Nucleotides / Cylinders/Stubs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  
No visible Surface models selected  

> select /E:16

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

> select clear

> save /home/taysa.bassani/image1.png width 1273 height 793 supersample 4

> movie record

> turn y 2 180

> wait 180

> movie encode /home/taysa.bassani/Desktop/movie1.mp4

Movie saved to /home/taysa.bassani/Desktop/movie1.mp4  
  

> save /home/taysa.bassani/Desktop/image1.png supersample 3

> movie record

> movie stop

> movie record

> view p1 wait 10; fly 50 p1 p2; wait 50; fly p2 p3; crossfade; wait 50; turn
> y 1 180; wait 180; movie encode test.mp4

Expected an objects specifier or a view name or a keyword  

> movie record

Already recording a movie  

> movie stop

> ui tool show "Find Cavities"

> split #1 chains

Split 1fmo (#1) into 2 models  
Chain information for 1fmo E #1.1  
---  
Chain | Description  
E | No description available  
  
Chain information for 1fmo I #1.2  
---  
Chain | Description  
I | No description available  
  

> close session

> open 1fmo format mmcif fromDatabase pdb

1fmo title:  
Crystal structure of A polyhistidine-tagged recombinant catalytic subunit of
camp-dependent protein kinase complexed with the peptide inhibitor pki(5-24)
and adenosine [more info...]  
  
Chain information for 1fmo #1  
---  
Chain | Description | UniProt  
E | CAMP-DEPENDENT PROTEIN KINASE | KAPCA_MOUSE 1-350  
I | HEAT STABLE RABBIT SKELETAL MUSCLE INHIBITOR PROTEIN | IPKA_RABIT 5-24  
  
Non-standard residues in 1fmo #1  
---  
ADN — adenosine  
  

> split #1 chains

Split 1fmo (#1) into 2 models  
Chain information for 1fmo E #1.1  
---  
Chain | Description  
E | No description available  
  
Chain information for 1fmo I #1.2  
---  
Chain | Description  
I | No description available  
  

> ui tool show "Find Cavities"

No structures chosen  

> kvfinder #1.1

18 cavities found for 1fmo E #1.1  
1fmo E Cavities  
---  
ID |  | Volume | Area | Points | Maximum  
Depth | Average  
Depth  
1.1.1.6 |  | 583.2 | 475.84 | 2700 | 10.73 | 3.7  
1.1.1.1 |  | 151.63 | 124.04 | 702 | 4.24 | 1.4  
1.1.1.13 |  | 147.1 | 169.48 | 681 | 0 | 0  
1.1.1.3 |  | 65.45 | 70.42 | 303 | 2.24 | 0.62  
1.1.1.4 |  | 59.62 | 69.8 | 276 | 3 | 0.77  
1.1.1.2 |  | 52.27 | 61.4 | 242 | 3 | 0.94  
1.1.1.10 |  | 50.54 | 59.05 | 234 | 3.06 | 1.17  
1.1.1.8 |  | 35.21 | 51.35 | 163 | 2.75 | 1.05  
1.1.1.12 |  | 29.38 | 44.82 | 136 | 1.2 | 0.33  
1.1.1.7 |  | 24.84 | 42.18 | 115 | 3.06 | 1.76  
1.1.1.16 |  | 19.01 | 26.44 | 88 | 1.8 | 0.64  
1.1.1.14 |  | 13.18 | 28.05 | 61 | 1.8 | 0.87  
1.1.1.9 |  | 12.31 | 29.54 | 57 | 0 | 0  
1.1.1.11 |  | 12.31 | 29.54 | 57 | 0 | 0  
1.1.1.17 |  | 11.02 | 17.49 | 51 | 0.85 | 0.29  
1.1.1.15 |  | 10.58 | 23.85 | 49 | 1.7 | 0.8  
1.1.1.5 |  | 10.37 | 19.57 | 48 | 0.85 | 0.19  
1.1.1.18 |  | 9.29 | 15.91 | 43 | 0.6 | 0.13  
  

> color byattribute a:kvfinder_depth #1.1.1.1-8,10,12,14-18

5211 atoms, 15 residues, atom kvfinder_depth range 0 to 10.7  

> select add #1.1

8900 atoms, 2884 bonds, 440 residues, 20 models selected  

> select add #1

9064 atoms, 3043 bonds, 467 residues, 22 models selected  

> select subtract #1

Nothing selected  

> select add #1.1

8900 atoms, 2884 bonds, 440 residues, 20 models selected  

> view #1.1.1.6 @< 3.5

> zoom 0.75

moved plane near -36.67727843162242 [-0.16798755 0.31484129 0.93416013]  
moved plane far -36.67727843162242 [-0.16798755 0.31484129 0.93416013]  

> surface #1.1.1.1-18 transparency 50

> color #1.1.1.1-18 fromatoms transparency 50

> ~surface #1.1.1

> surface #1.1.1.6

> show
> #!1.1/E:49-57,70,72,74,84,87-88,91,104,120-123,127,166,168,170-171,173,183-184,186-187,200-201,327

> view #!1.1.1.1 @< 3.5

> zoom 0.75

moved plane near -23.81630212299434 [-0.16798755 0.31484129 0.93416013]  
moved plane far -23.81630212299434 [-0.16798755 0.31484129 0.93416013]  

> ~surface #1.1.1

> surface #!1.1.1.1

> show #!1.1/E:14-15,18-19,100,152,155-156,292,302-303,306

> view #!1.1.1.6 @< 3.5

> zoom 0.75

moved plane near -36.97418419029915 [-0.16798755 0.31484129 0.93416013]  
moved plane far -36.97418419029915 [-0.16798755 0.31484129 0.93416013]  

> ~surface #1.1.1

> surface #!1.1.1.6

> show
> #!1.1/E:49-57,70,72,74,84,87-88,91,104,120-123,127,166,168,170-171,173,183-184,186-187,200-201,327

> help help:user

> help help:quickstart

> kvfinder #1.1 boxOrigin 0,4, -2 boxExtent 15,10,10

1 cavities found for 1fmo E #1.1  
1fmo E Cavities  
---  
ID |  | Volume | Area | Points | Maximum  
Depth | Average  
Depth  
1.1.1.1 |  | 418.39 | 300.44 | 1937 | 7.25 | 2.47  
  

> view #1.1.1.1 @< 3.5

> zoom 0.75

moved plane near -33.54657113040634 [-0.75630043 -0.103922 -0.64591787]  
moved plane far -33.54657113040634 [-0.75630043 -0.103922 -0.64591787]  

> surface #1.1.1.1 transparency 50

> ~surface #1.1.1

> surface #1.1.1.1

> show
> #!1.1/E:49-57,70,72,74,104,120-123,127,166,168,170-171,173,183-184,327,330

> color #1.1.1.1 #f8e45c

> color #1.1.1.1 #ffffff

> color #1.1.1.1 #dc8add

> color #1.1.1.1 #ed333b

> color #1.1.1.1 #ffbe6f

> color #1.1.1.1 #ffa348

> color #1.1.1.1 #f8e45c

> color #1.1.1.1 #f6d32d

> select add #1.1

4831 atoms, 2884 bonds, 423 residues, 3 models selected  

> select subtract #1.1

1 model selected  

> select add #1.1

4831 atoms, 2884 bonds, 423 residues, 3 models selected  

> select subtract #1.1

1 model selected  

> select add #1.2

164 atoms, 159 bonds, 27 residues, 1 model selected  

> select subtract #1.2

Nothing selected  

> select add #1.1

4831 atoms, 2884 bonds, 423 residues, 3 models selected  

> select subtract #1.1

1 model selected  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data  
val = col.display_value(item)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 886, in display_value  
val = self.value(instance)  
^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 903, in value  
return self.data_fetch(instance)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/kvfinder/tool.py", line 201, in color_func  
if s.display and s.atoms.displays.any():  
^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 529, in _get_display  
return Model.display.fget(self)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
^^^^^^^^^^^^^^^^^^^^  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data  
val = col.display_value(item)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 886, in display_value  
val = self.value(instance)  
^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 903, in value  
return self.data_fetch(instance)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/kvfinder/tool.py", line 201, in color_func  
if s.display and s.atoms.displays.any():  
^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 529, in _get_display  
return Model.display.fget(self)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
^^^^^^^^^^^^^^^^^^^^  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data  
val = col.display_value(item)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 886, in display_value  
val = self.value(instance)  
^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 903, in value  
return self.data_fetch(instance)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/kvfinder/tool.py", line 201, in color_func  
if s.display and s.atoms.displays.any():  
^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 529, in _get_display  
return Model.display.fget(self)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
^^^^^^^^^^^^^^^^^^^^  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data  
val = col.display_value(item)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 886, in display_value  
val = self.value(instance)  
^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 903, in value  
return self.data_fetch(instance)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/kvfinder/tool.py", line 201, in color_func  
if s.display and s.atoms.displays.any():  
^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 529, in _get_display  
return Model.display.fget(self)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
^^^^^^^^^^^^^^^^^^^^  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data  
val = col.display_value(item)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 886, in display_value  
val = self.value(instance)  
^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 903, in value  
return self.data_fetch(instance)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/kvfinder/tool.py", line 201, in color_func  
if s.display and s.atoms.displays.any():  
^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 529, in _get_display  
return Model.display.fget(self)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
^^^^^^^^^^^^^^^^^^^^  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data  
val = col.display_value(item)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 886, in display_value  
val = self.value(instance)  
^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 903, in value  
return self.data_fetch(instance)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/kvfinder/tool.py", line 201, in color_func  
if s.display and s.atoms.displays.any():  
^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 529, in _get_display  
return Model.display.fget(self)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
^^^^^^^^^^^^^^^^^^^^  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data  
val = col.display_value(item)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 886, in display_value  
val = self.value(instance)  
^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 903, in value  
return self.data_fetch(instance)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/kvfinder/tool.py", line 201, in color_func  
if s.display and s.atoms.displays.any():  
^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 529, in _get_display  
return Model.display.fget(self)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
^^^^^^^^^^^^^^^^^^^^  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data  
val = col.display_value(item)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 886, in display_value  
val = self.value(instance)  
^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 903, in value  
return self.data_fetch(instance)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/kvfinder/tool.py", line 201, in color_func  
if s.display and s.atoms.displays.any():  
^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 529, in _get_display  
return Model.display.fget(self)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
^^^^^^^^^^^^^^^^^^^^  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data  
val = col.display_value(item)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 886, in display_value  
val = self.value(instance)  
^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 903, in value  
return self.data_fetch(instance)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/kvfinder/tool.py", line 201, in color_func  
if s.display and s.atoms.displays.any():  
^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 529, in _get_display  
return Model.display.fget(self)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
^^^^^^^^^^^^^^^^^^^^  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data  
val = col.display_value(item)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 886, in display_value  
val = self.value(instance)  
^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 903, in value  
return self.data_fetch(instance)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/kvfinder/tool.py", line 201, in color_func  
if s.display and s.atoms.displays.any():  
^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 529, in _get_display  
return Model.display.fget(self)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
^^^^^^^^^^^^^^^^^^^^  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data  
val = col.display_value(item)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 886, in display_value  
val = self.value(instance)  
^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 903, in value  
return self.data_fetch(instance)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/kvfinder/tool.py", line 201, in color_func  
if s.display and s.atoms.displays.any():  
^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 529, in _get_display  
return Model.display.fget(self)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
^^^^^^^^^^^^^^^^^^^^  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data  
val = col.display_value(item)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 886, in display_value  
val = self.value(instance)  
^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 903, in value  
return self.data_fetch(instance)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/kvfinder/tool.py", line 201, in color_func  
if s.display and s.atoms.displays.any():  
^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 529, in _get_display  
return Model.display.fget(self)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
^^^^^^^^^^^^^^^^^^^^  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data  
val = col.display_value(item)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 886, in display_value  
val = self.value(instance)  
^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 903, in value  
return self.data_fetch(instance)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/kvfinder/tool.py", line 201, in color_func  
if s.display and s.atoms.displays.any():  
^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 529, in _get_display  
return Model.display.fget(self)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
^^^^^^^^^^^^^^^^^^^^  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data  
val = col.display_value(item)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 886, in display_value  
val = self.value(instance)  
^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 903, in value  
return self.data_fetch(instance)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/kvfinder/tool.py", line 201, in color_func  
if s.display and s.atoms.displays.any():  
^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 529, in _get_display  
return Model.display.fget(self)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
^^^^^^^^^^^^^^^^^^^^  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data  
val = col.display_value(item)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 886, in display_value  
val = self.value(instance)  
^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 903, in value  
return self.data_fetch(instance)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/kvfinder/tool.py", line 201, in color_func  
if s.display and s.atoms.displays.any():  
^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 529, in _get_display  
return Model.display.fget(self)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
^^^^^^^^^^^^^^^^^^^^  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data  
val = col.display_value(item)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 886, in display_value  
val = self.value(instance)  
^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 903, in value  
return self.data_fetch(instance)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/kvfinder/tool.py", line 201, in color_func  
if s.display and s.atoms.displays.any():  
^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 529, in _get_display  
return Model.display.fget(self)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
^^^^^^^^^^^^^^^^^^^^  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data  
val = col.display_value(item)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 886, in display_value  
val = self.value(instance)  
^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 903, in value  
return self.data_fetch(instance)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/kvfinder/tool.py", line 201, in color_func  
if s.display and s.atoms.displays.any():  
^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 529, in _get_display  
return Model.display.fget(self)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
^^^^^^^^^^^^^^^^^^^^  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 34, in data  
val = col.display_value(item)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 886, in display_value  
val = self.value(instance)  
^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_table.py", line 903, in value  
return self.data_fetch(instance)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/kvfinder/tool.py", line 201, in color_func  
if s.display and s.atoms.displays.any():  
^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 529, in _get_display  
return Model.display.fget(self)  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
^^^^^^^^^^^^^^^^^^^^  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.6 (Core Profile) Mesa 25.0.7-0ubuntu0.24.04.2
OpenGL renderer: Mesa Intel(R) Iris(R) Xe Graphics (ADL GT2)
OpenGL vendor: Intel

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: xcb

XDG_SESSION_TYPE=wayland
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
WAYLAND_DISPLAY=wayland-0
GNOME_SETUP_DISPLAY=:1
DISPLAY=:0
Manufacturer: LENOVO
Model: 21E40015BO
OS: Ubuntu 24.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 12 12th Gen Intel(R) Core(TM) i7-1255U
Cache Size: 12288 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            15Gi       5.0Gi       6.6Gi       796Mi       4.4Gi        10Gi
	Swap:          4.0Gi          0B       4.0Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation Alder Lake-UP3 GT2 [Iris Xe Graphics] [8086:46a8] (rev 0c)	
	Subsystem: Lenovo Alder Lake-UP3 GT2 [Iris Xe Graphics] [17aa:50a0]	
	Kernel driver in use: i915

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.6.1
    build: 1.2.2.post1
    certifi: 2025.7.14
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.19
    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: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.1
    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: 1.1.4
    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: 2.5.1
    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: 1.6.2
    ChimeraX-Label: 1.1.14
    ChimeraX-LinuxSupport: 1.0.1
    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: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    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
    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: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    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: 1.1.3
    ChimeraX-ProfileGrids: 1.1.3
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    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: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    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-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    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: 2.5.2
    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: 1.45.2
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.10.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.15
    decorator: 5.2.1
    distro: 1.9.0
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.59.0
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.3.2
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    narwhals: 2.9.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 2.3.4
    numpy: 1.26.4
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.2.0
    OpenMM-CUDA-12: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    plotly: 6.3.1
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    Pygments: 2.18.0
    pyKVFinder: 0.8.3
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    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: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tomlkit: 0.13.3
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.1
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14

[Eric Pettersen]

Duplicate of #18297