Histogram: `bins` must be positive, when an integer

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> C:\Users\Zuijderveltjl\Documents\LACDR\ASXL1\AlphaFold2\Human\ASXL1_WT.pdb
> format pdb

ASXL1_WT.pdb title:  
Alphafold monomer V2.0 prediction for polycomb group protein ASXL1 (Q8IXJ9)
[more info...]  
  
Chain information for ASXL1_WT.pdb #1  
---  
Chain | Description | UniProt  
A | polycomb group protein ASXL1 | ASXL1_HUMAN 1-1541  
  

> hide #1:450-1541

> select #1:450-1541

8109 atoms, 8291 bonds, 1092 residues, 1 model selected  

> hide sel

> delete sel

> show atoms

> color sequenctial palette blue/cornflower/white/teal

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  
Fetching url
http://www.colourlovers.com/api/palettes?keywords=blue/cornflower/white/teal&format=json&numResults=100
failed:  
HTTP Error 500: Internal Server Error  
[Repeated 1 time(s)]Fetching url
http://www.colourlovers.com/api/palettes?keywords=cornflower/white/teal&format=json&numResults=100
failed:  
HTTP Error 500: Internal Server Error  
Fetching url
http://www.colourlovers.com/api/palettes?keywords=Cyan/white/maroon&format=json&numResults=100
failed:  
HTTP Error 500: Internal Server Error  
Fetching url
http://www.colourlovers.com/api/palettes?keywords=cyan/white/maroon&format=json&numResults=100
failed:  
HTTP Error 500: Internal Server Error  

> color sequential #1/A palette cyanmaroon

> select SER

Expected an objects specifier or a keyword  

> select residues ser

Invalid "residues" argument: Expected true or false (or 1 or 0)  

> select residues S

Invalid "residues" argument: Expected true or false (or 1 or 0)  

> select residues

Missing "residues" keyword's argument  

> residues?

Unknown command: residues?  

> residues?help residues

Unknown command: residues?help residues  

> help residues

No help found for 'residues'  

> select: Ser

Unknown command: select: Ser  

> select: S

Unknown command: select: S  

> select :SER

288 atoms, 248 bonds, 48 residues, 1 model selected  

> color yellow

> color sel yellow

> select clear

> select :TRH

Nothing selected  

> select :THR

154 atoms, 132 bonds, 22 residues, 1 model selected  

> Color sel Gold

Unknown command: Color sel Gold  

> Color sel gold

Unknown command: Color sel gold  

> Color sel khaki

Unknown command: Color sel khaki  

> Color sel orange

Unknown command: Color sel orange  

> color sel orange

> color sel gold

> select clear

> color THR red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color byresidue THR red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> select :THR

154 atoms, 132 bonds, 22 residues, 1 model selected  

> color sel coral

> select :TYR

84 atoms, 85 bonds, 7 residues, 1 model selected  

> color sel cornsilk

> select clear

> hide atoms

> show cartoons

> lighting soft

> lighting shadows true intensity 0.5

> set bgColor gray

> set bgColor black

> set bgColor white

> set bgColor gray

> select :TYR

84 atoms, 85 bonds, 7 residues, 1 model selected  

> color sel goldenrod

> color sel darkgoldenrod

> select clear

> close session

> open
> C:\Users\Zuijderveltjl\Documents\LACDR\ASXL1\AlphaFold2\Human\ASXL1_WT.pdb
> format pdb

ASXL1_WT.pdb title:  
Alphafold monomer V2.0 prediction for polycomb group protein ASXL1 (Q8IXJ9)
[more info...]  
  
Chain information for ASXL1_WT.pdb #1  
---  
Chain | Description | UniProt  
A | polycomb group protein ASXL1 | ASXL1_HUMAN 1-1541  
  

> color sequential A/#1 palette PRGn-5

Expected one of 'chains', 'polymers', 'residues', or 'structures' or a keyword  

> color sequential palette prgn-5

Fetching url
http://www.colourlovers.com/api/palettes?keywords=Cornflowerteal&format=json&numResults=100
failed:  
HTTP Error 500: Internal Server Error  

> color sequential palette Cornflower:white:teal

Invalid "palette" argument: Invalid color name or specifier  
Fetching url
http://www.colourlovers.com/api/palettes?keywords=cornflower/white/teal&format=json&numResults=100
failed:  
HTTP Error 500: Internal Server Error  
Fetching url
http://www.colourlovers.com/api/palettes?keywords=cornflower/teal&format=json&numResults=100
failed:  
HTTP Error 500: Internal Server Error  

> color sequential palette cornflower:white:teal

> color sequential palette blue:cornflower:gray:white:gray:pink:red

> show atoms

[Repeated 1 time(s)]

> hide atoms

> select coil

10312 atoms, 10505 bonds, 1385 residues, 1 model selected  

> color sel sequential greys-5

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color sel greys-5

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color sel Greys-5

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color sel sequentialGreys-5

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color sel sequential Greys-5

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color palette Greys-5 sel

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> colorsel palette Greys-5

Unknown command: colorsel palette Greys-5  

> color sel palette Greys-5

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color sel sequential palette Greys-5

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color sequential palette greys-5

> color sequential #1/isCoil palette greys-5

> color sequential #1/isHelix palette hotpink:magenta

> color sequential #1/isStrand palette hotpink:magenta

> select clear

> color sequential #1/ishelix palette hotpink:magenta

> color sequential #1/isHelix palette hotpink:magenta

> color sequential #1/isHelix palette cornflower:white:teal

> select #1/isHelix

Nothing selected  

> select helix

1124 atoms, 1122 bonds, 138 residues, 1 model selected  

> select clear

> select #1/helix

Nothing selected  

> select #1/Helix

Nothing selected  

> select Helix

Expected an objects specifier or a keyword  

> select helix

1124 atoms, 1122 bonds, 138 residues, 1 model selected  

> color sequential helix palette cornflower:white:teal

> select clear

Fetching url
http://www.colourlovers.com/api/palettes?keywords=hotpink&format=json&numResults=100
failed:  
HTTP Error 500: Internal Server Error  

> color sequential strand palette hotpink:magenta

> color sequential helix palette hotpink:magenta

> color sequential helix palette rdpu-5

> color sequential coil palette bluered

Fetching url
http://www.colourlovers.com/api/palettes?keywords=white&format=json&numResults=100
failed:  
HTTP Error 500: Internal Server Error  

> color coil white

> color sequential helix cornflower:teal

Expected one of 'chains', 'polymers', 'residues', or 'structures' or a keyword  

> color sequential helix palette cornflower:teal

> color sequential strand palette lightpink:coral

> color sequential coil palette mistyrose:lightgray

> color sequential coil palette lightgray:silver

> set bgColor white

> set bgColor gray

> color sequential coil palette gray:slategray

> set bgColor white

> color sequential coil palette gainsboro:slategray

> set bgColor gray

> color sequential coil palette slateblue:maroon

> color sequential coil palette paleturquoise:salmon

> color sequential coil palette paleturquoise::khaki:salmon

Invalid "palette" argument: Missing color name or specifier  

> color sequential coil palette paleturquoise:khaki:salmon

> color sequential coil palette paleturquoise:salmon

> color sequential coil palette paleturquoise:gray:salmon

> color sequential coil palette paleturquoise:slategray:salmon

> color sequential coil palette mistyrose:lightpink:lightcoral:lightsalmon

> color sequential coil palette mistyrose:slategray

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> select /A:2

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

> select /A:2-88

682 atoms, 692 bonds, 87 residues, 1 model selected  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> show sel atoms

> color byatom

> color sel helix teal

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> select clear

> select /A:264

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

> select /A:264-375

939 atoms, 958 bonds, 112 residues, 1 model selected  

> show sel atoms

> select clear

> select /A:614-615

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

> select /A:614-627

103 atoms, 102 bonds, 14 residues, 1 model selected  

> show sel atoms

> select /A:642

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select /A:642-1541

6627 atoms, 6772 bonds, 900 residues, 1 model selected  

> color sequential #1:404-1541 palette indianred:crimson:indianred

> select clear

> select :THR,SER,TYR

1860 atoms, 1651 bonds, 282 residues, 1 model selected  

> color sel yellow

> select clear

> rock

> delete #1:404:1541

> delete #1:404-1541

> stop

> select /A:1

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

> select /A:1

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

> color sel blue

> select /A:371-372

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select /A:371-375

41 atoms, 40 bonds, 5 residues, 1 model selected  

> select /A:379-380

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select /A:379-380

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select /A:381

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

> select /A:380-381

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select /A:403

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

> select /A:403

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

> color sel red

> select clear

> ~hbonds

> rock

> rockslow

Unknown command: rockslow  

> rock slow

Expected an axis vector or a keyword  

> help rock

> turn

[Repeated 3 time(s)]

> spin

Unknown command: spin  

> spinrock help

Unknown command: spinrock help  

> help rock

> set bgColor white

> set bgColor black

> set bgColor gray

> lighting simple

> lighting shadows true

> lighting soft

> lighting shadows true intensity 0.5

> stop

> turn

[Repeated 1 time(s)]

> rock

> select /A:34-50

129 atoms, 128 bonds, 17 residues, 1 model selected  

> select /A:34-55

161 atoms, 161 bonds, 22 residues, 1 model selected  

> select /A:53-54

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

> select /A:52-54

20 atoms, 20 bonds, 3 residues, 1 model selected  

> select /A:12

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

> select /A:12

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

> select /A:30

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

> select /A:30

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

> stop

> Color sequential #1/coil palette paleblue:lightgrey:lightpink

Unknown command: Color sequential #1/coil palette paleblue:lightgrey:lightpink  

> color sequential #1/coil palette paleblue:lightgrey:lightpink

Invalid "palette" argument: Invalid color name or specifier  

> color sequential #1/coil palette lightblue:lightgrey:lightpink

[Repeated 1 time(s)]

> select coil

2115 atoms, 2129 bonds, 284 residues, 1 model selected  

> color sequential sel palette lightblue:white:lightpink

> select clear

[Repeated 1 time(s)]

> select helix

888 atoms, 890 bonds, 107 residues, 1 model selected  

> color sequential sel palette cornflower:teal

> hide sel atoms

> select strand

112 atoms, 111 bonds, 12 residues, 1 model selected  

> color select salmon

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color bychain sel salmon

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color sequential sel palette salmon:hotpink

> select clear

> hide atoms

> show atoms

> hide atoms

> select helix:strand

Expected an objects specifier or a keyword  

> select helix

888 atoms, 890 bonds, 107 residues, 1 model selected  

> color byatom

> show sel atoms

> select strand

112 atoms, 111 bonds, 12 residues, 1 model selected  

> show sel atoms

> select 12

Expected an objects specifier or a keyword  

> select res12

Expected an objects specifier or a keyword  

> select :12

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

> select :12, 24

19 atoms, 18 bonds, 2 residues, 1 model selected  

> select :12, 24, 25, 30, 48, 51, 64, 79, 82, 105, 110, 117, 118, 120, 126,
> 130, 135, 137, 140, 146, 151, 155, 156, 165, 175, 191, 199, 201, 203, 204,
> 205, 206, 207, 209, 224, 254, 257, 262, 278, 304, 305, 306, 319, 359, 366

294 atoms, 260 bonds, 45 residues, 1 model selected  

> color sel yellow

> select clear

> rock

> select :422, 718, 1273

Nothing selected  

> color lime

> color sel lime

> show all

> hide all

> select :1

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

> color sel blue

> select :401

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

> select :404

Nothing selected  

> select :4043

Nothing selected  

> select :403

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

> color sel red

> select clear

> open C:/Users/Zuijderveltjl/Documents/LACDR/ASXL1/Disorder/pdb8h1t.ent

pdb8h1t.ent title:  
Cryo-em structure of BAP1-ASXL1 bound to chromatosome [more info...]  
  
Chain information for pdb8h1t.ent #2  
---  
Chain | Description | UniProt  
A E | histone H3.1 | H31_HUMAN 0-135  
B F | histone H4 | H4_HUMAN 0-102  
C G | histone H2A type 1-D | H2A1D_HUMAN 0-129  
D H | histone H2B type 2-E | H2B2E_HUMAN 0-125  
I | DNA (187-mer) |  
J | DNA (187-mer) |  
K | histone H1.4 | H14_HUMAN 0-218  
L | ubiquitin carboxyl-terminal hydrolase BAP1 | BAP1_HUMAN 1-729  
M | ubiquitin | UBB_HUMAN 1-76  
N | additional SEX combs-LIKE protein 1 | ASXL1_HUMAN 1-378  
  

> hide surfaces

> stop

> select
> #1/A:2-4,6-8,13-23,31-40,52-62,86-88,264-267,270-275,278-287,290-292,307-309,311-325,331-344,351-354,369-375

888 atoms, 890 bonds, 107 residues, 1 model selected  

> hide #!1 models

> hide #!2 surfaces

> hide #!2 cartoons

> hide #!2 atoms

[Repeated 1 time(s)]

> hide #!2 cartoons

> show #!2 cartoons

> show #!2 target m

[Repeated 1 time(s)]

> ui tool show "Show Sequence Viewer"

> sequence chain #2/N

Alignment identifier is 2/N  

> hide all

> select #2/N

903 atoms, 922 bonds, 109 residues, 1 model selected  

> color sel blue

> color grey

> color sel blue

> select clear

> select #2/N

903 atoms, 922 bonds, 109 residues, 1 model selected  

> color sel strand hotpink

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color strand hotpink

> color helix cornflowerblue

> color desel grey

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color deselect grey

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color deselect grey

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> select clear

> color grey

> select #2/N

903 atoms, 922 bonds, 109 residues, 1 model selected  

> color sol blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color sel blue

> select clear

> show #!1 models

> hide #!1 models

> show #!1 models

> undo

[Repeated 9 time(s)]

> show #!1 models

> centre

Unknown command: centre  

> center

Unknown command: center  

> ui mousemode right translate

> ui mousemode right select

> ui mousemode right "translate selected models"

> ui mousemode right "move picked models"

> select #2/N

903 atoms, 922 bonds, 109 residues, 1 model selected  

> select #1/A:363-378

123 atoms, 122 bonds, 16 residues, 1 model selected  

> select #1/A:61-378

2458 atoms, 2502 bonds, 318 residues, 1 model selected  

> select #2/N

903 atoms, 922 bonds, 109 residues, 1 model selected  

> color sel blue

> select #1/A:378

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

> select #1/A:1-378

2929 atoms, 2979 bonds, 378 residues, 1 model selected  

> color sel blue

> select #2/N

903 atoms, 922 bonds, 109 residues, 1 model selected  

> select #2/N

903 atoms, 922 bonds, 109 residues, 1 model selected  

> color :1 red

> select clear

> select #1/A:290

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

> select #1/A:290-321

254 atoms, 258 bonds, 32 residues, 1 model selected  

> select #1/A:277

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

> select #1/A:214-277

494 atoms, 502 bonds, 64 residues, 1 model selected  

> select #2/N:263-275,277-286,310-327,330-352

553 atoms, 563 bonds, 64 residues, 1 model selected  

> select #2/N:293-295,301-303

54 atoms, 52 bonds, 6 residues, 1 model selected  

> select #1/A:71-73,81-83,293-295,301-303

112 atoms, 111 bonds, 12 residues, 1 model selected  

> select
> #1/A:2-4,6-8,13-23,31-40,52-62,86-88,264-267,270-275,278-287,290-292,307-309,311-325,331-344,351-354,369-375

888 atoms, 890 bonds, 107 residues, 1 model selected  

> select #1/A:71-73,81-83,293-295,301-303

112 atoms, 111 bonds, 12 residues, 1 model selected  

> select
> #1/A:2-4,6-8,13-23,31-40,52-62,86-88,264-267,270-275,278-287,290-292,307-309,311-325,331-344,351-354,369-375

888 atoms, 890 bonds, 107 residues, 1 model selected  

> select #1/A:296

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #1/A:296-344

401 atoms, 407 bonds, 49 residues, 1 model selected  

> select

20480 atoms, 21527 bonds, 2 pseudobonds, 2060 residues, 3 models selected  

> select clear

> select #2/N:286

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

> select #2/N:286-303

143 atoms, 144 bonds, 18 residues, 1 model selected  

> select #2/N:247-248

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

> select #2/N:247-307

477 atoms, 485 bonds, 61 residues, 1 model selected  

> select #2/N:247

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #2/N:247-324

627 atoms, 640 bonds, 78 residues, 1 model selected  

> select #2/N:247

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #2/N:247-322

608 atoms, 621 bonds, 76 residues, 1 model selected  

> select #2/N:247

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #2/N:247-250

30 atoms, 29 bonds, 4 residues, 1 model selected  

> select #2/N:251

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

> select #2/N:251-306

442 atoms, 450 bonds, 56 residues, 1 model selected  

> select #2/N:265

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

> select #2/N:265-308

349 atoms, 355 bonds, 44 residues, 1 model selected  

> select #2/N:265-266

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #2/N:265-312

385 atoms, 392 bonds, 48 residues, 1 model selected  

> select #2/N:263

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

> select #2/N:263-265

27 atoms, 26 bonds, 3 residues, 1 model selected  

> select #2/N:263-275,277-286,310-327,330-352

553 atoms, 563 bonds, 64 residues, 1 model selected  

> select #2/N:265-266

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #2/N:265-309

357 atoms, 363 bonds, 45 residues, 1 model selected  

> color sel hotpink

> color sel green

> select #1/A:265

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

> select #1/A:265-309

357 atoms, 363 bonds, 45 residues, 1 model selected  

> color sel green

> select clear

> hide #!2 models

Drag select of 23 residues  

> view matrix models #1,1,0,0,-46.777,0,1,0,-6.0633,0,0,1,18.568

> select clear

> select #1/A:213

4 atoms, 3 bonds, 1 residue, 1 model selected  

> color sequential coil palette lightblue:white:lightpink

> select clear

> color :1blue

> color :1 blue

> color sequential helix palette cornflower:teal

> color sequential strand palette salmon:hotpink

> select :12, 24, 25, 30, 48, 51, 64, 79, 82, 105, 110, 117, 118, 120, 126,
> 130, 135, 137, 140, 146, 151, 155, 156, 165, 175, 191, 199, 201, 203, 204,
> 205, 206, 207, 209, 224, 254, 257, 262, 278, 304, 305, 306, 319, 359, 366

2385 atoms, 2327 bonds, 235 residues, 2 models selected  

> color sel yellow

> select clear

> lighting simple

> lighting soft

> lighting shadows true intensity 0.5

> select :403

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

> color sel red

> select clear

> select #1/A:265

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

> select #1/A:265-309

357 atoms, 363 bonds, 45 residues, 1 model selected  

> color sequential sel palette magenta:purple

> select clear

> select :12, 24, 25, 30, 48, 51, 64, 79, 82, 105, 110, 117, 118, 120, 126,
> 130, 135, 137, 140, 146, 151, 155, 156, 165, 175, 191, 199, 201, 203, 204,
> 205, 206, 207, 209, 224, 254, 257, 262, 278, 304, 305, 306, 319, 359, 366

2385 atoms, 2327 bonds, 235 residues, 2 models selected  

> color sel yellow

> select clear

> spin

Unknown command: spin  

> ui mousemode right "clip rotate"

> ui mousemode right rotate

> set bgColor white

> set bgColor #ffffff00

> color coil grey

> select :12, 24, 25, 30, 48, 51, 64, 79, 82, 105, 110, 117, 118, 120, 126,
> 130, 135, 137, 140, 146, 151, 155, 156, 165, 175, 191, 199, 201, 203, 204,
> 205, 206, 207, 209, 224, 254, 257, 262, 278, 304, 305, 306, 319, 359, 366

2385 atoms, 2327 bonds, 235 residues, 2 models selected  

> color sel orange

> select clear

> select #1/A:265-266

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #1/A:265-310

365 atoms, 371 bonds, 46 residues, 1 model selected  

> select clear

> select #1/A:265

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

> select #1/A:265-310

365 atoms, 371 bonds, 46 residues, 1 model selected  

> color sequential sel palette mediumblue:purple

> select clear

> select :12, 24, 25, 30, 48, 51, 64, 79, 82, 105, 110, 117, 118, 120, 126,
> 130, 135, 137, 140, 146, 151, 155, 156, 165, 175, 191, 199, 201, 203, 204,
> 205, 206, 207, 209, 224, 254, 257, 262, 278, 304, 305, 306, 319, 359, 366

2385 atoms, 2327 bonds, 235 residues, 2 models selected  

> color sel orange

> select clear

> select :1

54 atoms, 54 bonds, 4 residues, 2 models selected  

> color sel blue

> select :403

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

> color sel red

> select clear

> ui mousemode right "mark point"

> marker #3 position -32.58,10.23,-14.33 color yellow radius 1

> marker #3 position -27.91,-4.231,-16.37 color yellow radius 1

> undo

[Repeated 5 time(s)]

> redo

[Repeated 4 time(s)]

> ui mousemode right "mark center"

> delete marker

Missing or invalid "atoms" argument: invalid atoms specifier  

> delete markers

Missing or invalid "atoms" argument: invalid atoms specifier  

> select add #3

2 atoms, 2 residues, 1 model selected  

> hide #3 models

> select subtract #3

Nothing selected  

> save C:\Users\Zuijderveltjl\Desktop\image1.png supersample 3

> save C:\Users\Zuijderveltjl\Desktop\image2.png supersample 3

> save C:\Users\Zuijderveltjl\Desktop\image3.png supersample 3

> save C:\Users\Zuijderveltjl\Desktop\image4.png supersample 3

> lighting simple

> lighting shadows true

> lighting soft

> lighting shadows true intensity 0.5

> ui mousemode right translate

> ui mousemode right "translate selected models"

> rock

>

Incomplete command: movie  

> movie encode output C:\Users\Zuijderveltjl/Desktop/myMovie.mp4 format mp4

Invalid "format" argument: Should be one of 'apng', 'avi', 'h264', 'mov',
'ogg', 'ogv', 'qt', 'quicktime', 'theora', 'vp8', 'webm', or 'wmv'  

> movie encode output C:\Users\Zuijderveltjl/Desktop/myMovie.avi format avi

No frames have been recorded  

> record movie

Unknown command: record movie  

> movie record

> stop record

Expected fewer arguments  

> movie stop

> movie encode output C:\Users\Zuijderveltjl/Desktop/myMovie.avi format avi

Movie saved to C:\Users\Zuijderveltjl/Desktop/myMovie.avi  
  

> select #1/A:162

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

> select #1/A:162-165

34 atoms, 33 bonds, 4 residues, 1 model selected  

> select #1/A:162

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

> select #1/A:162-165

34 atoms, 33 bonds, 4 residues, 1 model selected  

> select
> #1/A:2-4,6-8,13-23,31-40,52-62,86-88,264-267,270-275,278-287,290-292,307-309,311-325,331-344,351-354,369-375

888 atoms, 890 bonds, 107 residues, 1 model selected  

> select #1/A:1

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

> select #1/A:1-67

520 atoms, 526 bonds, 67 residues, 1 model selected  

> stop

> view matrix models #1,1,0,0,-44.831,0,1,0,6.1138,0,0,1,19.088

> view matrix models #1,1,0,0,-43.856,0,1,0,2.628,0,0,1,18.805

> view matrix models #1,1,0,0,-42.883,0,1,0,-0.62429,0,0,1,18.535

> select clear

> ui mousemode right rotate

> ui mousemode right select

Drag select of 7 residues  
Drag select of 11 residues  
Drag select of 8 residues  
Drag select of 9 residues  

> select #1/A:14

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

> select #1/A:14-26

101 atoms, 101 bonds, 13 residues, 1 model selected  

> select #1/A:13

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

> select #1/A:23

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

> select #1/A:40

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

> select #1/A:31

7 atoms, 7 bonds, 1 residue, 1 model selected  
Drag select of 1 residues  

> select #1/A:83

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

> select #1/A:81

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

> select #1/A:83

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

> select #1/A:81

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

> select #1/A:71

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

> select #1/A:73

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

> select clear

> ui mousemode right "translate selected models"

> ui mousemode right select

> select #1/A:376

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #1/A:376

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #1/A:375

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

> select #1/A:369

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

> select clear

[Repeated 1 time(s)]

> select #1/A:351

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

> select #1/A:354

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

> select #1/A:344

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

> select #1/A:332

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

> select #1/A:325

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

> select #1/A:311

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

> select :12, 24, 25, 30, 48, 51, 64, 79, 82, 105, 110, 117, 118, 120, 126,
> 130, 135, 137, 140, 146, 151, 155, 156, 165, 175, 191, 199, 201, 203, 204,
> 205, 206, 207, 209, 224, 254, 257, 262, 278, 304, 305, 306, 319, 359, 366

2385 atoms, 2327 bonds, 235 residues, 2 models selected  

> select #1/A:264

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

> select #1/A:310

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

> select #1/A:310

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

> select #1/A:264-310

373 atoms, 379 bonds, 47 residues, 1 model selected  

> hide #!1 models

> open
> C:/Users/Zuijderveltjl/Documents/LACDR/ASXL1/AlphaFold2/Interactions/ASXL1_RARA_9d8dd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb

Chain information for
ASXL1_RARA_9d8dd_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb
#4  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> rename #4 ASXL:RAR

> rename #4 ASX1L:RARA

> ui tool show "Show Sequence Viewer"

> sequence chain #4/A

Alignment identifier is 4/A  

> sequence chain #4/B

Alignment identifier is 4/B  

> select #4/A:1-2

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select #4/A:1-70

541 atoms, 547 bonds, 70 residues, 1 model selected  

> select #4/A:1

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

> select #4/A

4007 atoms, 4078 bonds, 520 residues, 1 model selected  

> color sequential lightgrey

Expected one of 'chains', 'polymers', 'residues', or 'structures' or a keyword  

> color sel lightgrey

> select clear

> select #4/a

4007 atoms, 4078 bonds, 520 residues, 1 model selected  

> color sel gray

> select #4/1:1

Nothing selected  

> color sel blue

> select #4/A:520

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

> select #4/A:520

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

> color sel red

> select clear

[Repeated 1 time(s)]

> select #4/A:1-2

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select #4/A:1

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

> color sel blue

> select #4/A:350

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

> color sequential helix palette corflower:teal

Invalid "palette" argument: Invalid color name or specifier  

> color sequential helix palette cornflower:teal

> color sequential #4/a helix palette cornflower:teal

Expected one of 'chains', 'polymers', 'residues', or 'structures' or a keyword  

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> color sequential #4/: helix palette cornflower:teal

Expected one of 'chains', 'polymers', 'residues', or 'structures' or a keyword  

> color structures sequential #4/: helix palette cornflower:teal

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> select #4/b helix

Expected a keyword  

> select #4/b helices

Expected a keyword  

> select #4/b

3547 atoms, 3628 bonds, 462 residues, 1 model selected  

> color sel gray

> select clear

> select #4/b

3547 atoms, 3628 bonds, 462 residues, 1 model selected  

> select #4/b coil

Expected a keyword  

> select #4/b :coil

Nothing selected  

> select #4/b :helix

Nothing selected  

> select #4/b:helix

Nothing selected  

> select #4/b:strand

Nothing selected  

> select #4/B:strand

Nothing selected  

> select #4/A:/isHelix

Expected an objects specifier or a keyword  

> select #4/A :/isHelix

Expected a keyword  

> select #4/A /isHelix

4007 atoms, 4078 bonds, 520 residues, 1 model selected  

> select #4/A isHelix

Expected a keyword  

> select #4/A/Helix

4007 atoms, 4078 bonds, 520 residues, 1 model selected  

> select #4/A-helix

7554 atoms, 7706 bonds, 982 residues, 1 model selected  

> select #4/A

4007 atoms, 4078 bonds, 520 residues, 1 model selected  

> helix

Unknown command: helix  

> select #4/A :helix

Nothing selected  

> select #4/A:/isHelix

Expected an objects specifier or a keyword  

> select #4/A & :/structure=helix

Expected a keyword  

> select #4/A&helix

1110 atoms, 1117 bonds, 133 residues, 1 model selected  

> select #4/A&strand

112 atoms, 111 bonds, 12 residues, 1 model selected  

> color sequential sel palette salmon:hotpink

> select #4/b&coil

1934 atoms, 1974 bonds, 259 residues, 1 model selected  

> color sel black

> select #4/b&helix

1524 atoms, 1534 bonds, 191 residues, 1 model selected  

> color sequential sel palette purple:magenta

> select #4/b&strand

89 atoms, 87 bonds, 12 residues, 1 model selected  

> color sequential sel palette maroon:red

> select clear

> color sequential sel palette yellow:orange

> color sequential #4/b&strand palette yellow:orange

> select #4 helix

Expected a keyword  

> select #4

7554 atoms, 7706 bonds, 982 residues, 1 model selected  

> select #4&helix

2634 atoms, 2651 bonds, 324 residues, 1 model selected  

> show sel atoms

> color byattribute atom

No known/registered numeric attribute atom  

> color byatom

> select clear

Drag select of 11 atoms, 7 residues, 10 bonds  

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models #4,1,0,0,3.0388,0,1,0,-13.826,0,0,1,-4.9699

> view matrix models #4,1,0,0,6.4857,0,1,0,-28.643,0,0,1,-10.041

> view matrix models #4,1,0,0,15.544,0,1,0,-36.534,0,0,1,-3.0417

> view matrix models #4,1,0,0,14.487,0,1,0,-32.625,0,0,1,-1.9021

> set bgColor gray

> set bgColor #80808000

> desel

Unknown command: desel  

> deseldeselect

Unknown command: deseldeselect  

> deselect

Unknown command: deselect  

> deselectdes

Unknown command: deselectdes  

> des

Unknown command: des  

> desunselect

Unknown command: desunselect  

> unselect

Unknown command: unselect  

> hide sel atoms

> select #4

7554 atoms, 7706 bonds, 982 residues, 1 model selected  

> hide sel atoms

> view matrix models #4,1,0,0,8.2735,0,1,0,-30.826,0,0,1,7.4488

> findclash #4

Unknown command: findclash #4  

> findclash?

Unknown command: findclash?  

> findclash?help findclash

Unknown command: findclash?help findclash  

> help findclash

No help found for 'findclash'  

> help contact

[Repeated 1 time(s)]

> show hbonds

[Repeated 1 time(s)]

> select contacts

Expected an objects specifier or a keyword  

> select contacts chains

Expected an objects specifier or a keyword  

> select contacts #4/a to #4/b

Expected an objects specifier or a keyword  

> select contacts #4/a&#4/b

Expected an objects specifier or a keyword  

> select contacts #4

Expected an objects specifier or a keyword  

> contacts

20572 contacts  

> hide #5 models

> contacts #4/A #4/B

5061 contacts  

> show contact #4/A #4/B

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> Contacts #4/A #4/B

Unknown command: Contacts #4/A #4/B  

> Contact #4/A #4/B

Unknown command: Contact #4/A #4/B  

> Contact #4/A to #4/B

Unknown command: Contact #4/A to #4/B  

> Contacts #4/A to #4/B

Unknown command: Contacts #4/A to #4/B  

> Contacts #4/A-#4/B

Unknown command: Contacts #4/A-#4/B  

> Contacts #4/A:#4/B

Unknown command: Contacts #4/A:#4/B  

> Contacts #4/A&#4/B

Unknown command: Contacts #4/A&#4/B  

> ui mousemode right select

> select #4/A:385

4 atoms, 3 bonds, 1 residue, 1 model selected  
Drag select of 5 residues  

> select #4/A:385

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #4/A:386

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

> select #4/A:331

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

> select #4/A:386

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

> select #4/A:367

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

> select #4/A:248-367

998 atoms, 1019 bonds, 969 pseudobonds, 120 residues, 2 models selected  

> select
> #4/A:3-10,13-23,31-40,52-64,84-90,258-260,264-267,270-274,278-287,290-292,311-326,331-353,367-386

1110 atoms, 1117 bonds, 692 pseudobonds, 133 residues, 2 models selected  

> select #4/A:265

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

> select #4/A:265-266

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #4/A:264-265

19 atoms, 18 bonds, 2 residues, 1 model selected  

> select #4/A:264-267

32 atoms, 31 bonds, 4 pseudobonds, 4 residues, 2 models selected  

> select #4/A:332

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

> select #4/A:332-340

81 atoms, 80 bonds, 59 pseudobonds, 9 residues, 2 models selected  

> select
> #4/A:3-10,13-23,31-40,52-64,84-90,258-260,264-267,270-274,278-287,290-292,311-326,331-353,367-386

1110 atoms, 1117 bonds, 692 pseudobonds, 133 residues, 2 models selected  

> select #4/A:340

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

> select #4/A:331-340

91 atoms, 91 bonds, 64 pseudobonds, 10 residues, 2 models selected  

> select #4/A:331

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

> select #4/A:324-331

62 atoms, 63 bonds, 18 pseudobonds, 8 residues, 2 models selected  

> select #4/A:332-333

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select #4/A:332-354

211 atoms, 213 bonds, 276 pseudobonds, 23 residues, 2 models selected  

> select #4/A:331

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

> select #4/A:331-353

210 atoms, 212 bonds, 251 pseudobonds, 23 residues, 2 models selected  

> select #4/A:367

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

> select #4/A:367-386

154 atoms, 153 bonds, 68 pseudobonds, 20 residues, 2 models selected  

> select #4/A:331

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

> select #4/A:331-386

476 atoms, 482 bonds, 499 pseudobonds, 56 residues, 2 models selected  

> show sel atoms

> select #4/A:391

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

> select #4/A:391-433

366 atoms, 370 bonds, 84 pseudobonds, 43 residues, 2 models selected  

> select #4/A:354

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

> select #4/A:354-366

112 atoms, 115 bonds, 88 pseudobonds, 13 residues, 2 models selected  

> hide sel atoms

> show sel atoms

> select #4/B:223

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

> select #4/B:222

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

> select #4/B:222-245

199 atoms, 202 bonds, 90 pseudobonds, 24 residues, 2 models selected  

> show sel atoms

> select #4/B:254

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

> select #4/B:182

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

> select #4/B:182-183

16 atoms, 16 bonds, 2 residues, 1 model selected  

> select #4/B:182-198

137 atoms, 138 bonds, 54 pseudobonds, 17 residues, 2 models selected  

> show sel atoms

> select #4/B:346

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

> select #4/B:345

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

> select #4/B:345-366

186 atoms, 188 bonds, 65 pseudobonds, 22 residues, 2 models selected  

> show sel atoms

> select #4/B:251

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

> select #4/B:249

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

> select #4/B:249-251

25 atoms, 25 bonds, 1 pseudobond, 3 residues, 2 models selected  

> show sel atoms

> select clear

[Repeated 2 time(s)]

> select #4/B:254

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

> select #4/B:254

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

> select #4/B:254-255

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

> select #4/B:254-260

53 atoms, 52 bonds, 15 pseudobonds, 7 residues, 2 models selected  

> select #4/B:254

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

> select #4/B:254-276

177 atoms, 176 bonds, 76 pseudobonds, 23 residues, 2 models selected  

> select #4/B:366

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

> select #4/B:366

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

> select #4/B:329-366

307 atoms, 309 bonds, 132 pseudobonds, 38 residues, 2 models selected  

> select #4/B:366-367

22 atoms, 21 bonds, 3 pseudobonds, 2 residues, 2 models selected  

> select #4/B:351-366

137 atoms, 138 bonds, 42 pseudobonds, 16 residues, 2 models selected  

> hide sel atoms

> select #4/B:351

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

> show sel atoms

> set bgColor white

> set bgColor #ffffff00

> lighting soft

> lighting shadows true intensity 0.5

> select #4/A:332

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

> select
> #4/A:3-10,13-23,31-40,52-64,84-90,258-260,264-267,270-274,278-287,290-292,311-326,331-353,367-386

1110 atoms, 1117 bonds, 692 pseudobonds, 133 residues, 2 models selected  

> select #4/A:321

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

> select #4/A:321-327

56 atoms, 55 bonds, 18 pseudobonds, 7 residues, 2 models selected  

> select #4/A:311

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

> select #4/A:311-327

143 atoms, 147 bonds, 64 pseudobonds, 17 residues, 2 models selected  

> select #4/A:331

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

> select #4/A:331-353

210 atoms, 212 bonds, 251 pseudobonds, 23 residues, 2 models selected  

> select #4/A:331

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

> select #4/A:331-386

476 atoms, 482 bonds, 499 pseudobonds, 56 residues, 2 models selected  

> select #4/B:222

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

> select #4/B:222-245

199 atoms, 202 bonds, 90 pseudobonds, 24 residues, 2 models selected  

> select #4/B:346

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

> select #4/B:222

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

> select #4/B:222-366

1144 atoms, 1161 bonds, 742 pseudobonds, 145 residues, 2 models selected  

> clashes #4/A:331-386 #4/B:222-366

134 clashes  
Drag select of 4 residues  

> ui mousemode right "move picked models"

> contacts #4/A:331-386 #4/B:222-366

1828 contacts  

> show #5 models

> contacts #4/A:331-386 #4/B:222-366

1828 contacts  

> contacts #4/A #4/B distanceOnly 4.0

9011 distances  

> select add #5

30 atoms, 9011 pseudobonds, 4 residues, 2 models selected  

> select subtract #5

30 atoms, 4 residues, 1 model selected  

> select add #5

30 atoms, 9011 pseudobonds, 4 residues, 2 models selected  

> select add #4

7554 atoms, 7706 bonds, 9145 pseudobonds, 982 residues, 3 models selected  

> select subtract #4

Nothing selected  

> delete sel

> select add #5

9011 pseudobonds, 1 model selected  

> delete

Missing or invalid "atoms" argument: empty atom specifier  

> delete contacts

Missing or invalid "atoms" argument: invalid atoms specifier  

> delete contact

Missing or invalid "atoms" argument: invalid atoms specifier  

> delete sel

> select subtract #5

Nothing selected  

> contacts #4/A #4/B

5061 contacts  

> from chimerax.atomic import selected_atoms

Unknown command: from chimerax.atomic import selected_atoms  

> atoms = selected_atoms(session)

Unknown command: atoms = selected_atoms(session)  

> contacts = []

Missing or invalid "testAtoms" argument: invalid atoms specifier  

> force atom1 in atoms:

force is provided by the uninstalled bundle SEQCROW versions 1.6.6 – 1.8.1  

> force atom2 in atoms:

force is provided by the uninstalled bundle SEQCROW versions 1.6.6 – 1.8.1  

> if atom1.residue != atom2.residue and atom1.structure != atom2.structure:

Unknown command: if atom1.residue != atom2.residue and atom1.structure !=
atom2.structure:  

> distance = atom1.coord.distance(atom2.coord)

Missing or invalid "objects" argument: invalid objects specifier  

> if distance < 4.0: # or your specific cutoff

Unknown command: if distance < 4.0: # or your specific cutoff  

> contacts.append((atom1, atom2, distance))

Unknown command: contacts.append((atom1, atom2, distance))  

> force c in contacts:

force is provided by the uninstalled bundle SEQCROW versions 1.6.6 – 1.8.1  

> print(c)

Unknown command: print(c)  

> undo

Undo failed, probably because structures have been modified.  

> undo

Undo failed, probably because structures have been modified.  

> hide #5 models

> view matrix models #4,1,0,0,4.6582,0,1,0,-33.654,0,0,1,14.946

> select #4/A:330

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

> select #4/A:1-330

2511 atoms, 2554 bonds, 1405 pseudobonds, 330 residues, 2 models selected  

> hide sel cartoons

> select
> #4/A:3-10,13-23,31-40,52-64,84-90,258-260,264-267,270-274,278-287,290-292,311-326,331-353,367-386

1110 atoms, 1117 bonds, 718 pseudobonds, 133 residues, 3 models selected  

> select #4/A:387

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

> select #4/A:387-389

20 atoms, 20 bonds, 4 pseudobonds, 3 residues, 2 models selected  

> select #4/A:387

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

> select #4/A:387-520

1020 atoms, 1040 bonds, 280 pseudobonds, 134 residues, 2 models selected  

> hide sel cartoons

> select #4/B:221

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

> select #4/B:1-221

1710 atoms, 1756 bonds, 685 pseudobonds, 221 residues, 2 models selected  

> hide sel cartoons

> select #4/B:382

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

> select #4/B:382-385

34 atoms, 33 bonds, 1 pseudobond, 4 residues, 2 models selected  

> select #4/B:222

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

> select #4/B:222

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

> select #4/B:222

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

> select #4/B:222-366

1144 atoms, 1161 bonds, 747 pseudobonds, 145 residues, 3 models selected  

> select #4/B:367

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

> select #4/B:367-462

693 atoms, 709 bonds, 252 pseudobonds, 96 residues, 2 models selected  

> hide sel cartoons

> select #4/B:277

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

> select #4/B:277-290

111 atoms, 113 bonds, 44 pseudobonds, 14 residues, 2 models selected  

> select #4/B:277

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

> select #4/B:277-334

443 atoms, 451 bonds, 262 pseudobonds, 58 residues, 3 models selected  

> hide sel surfaces

> hide sel cartoons

> ui mousemode right select

> select #4/B:255

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

> show sel atoms

> select #4/B:254

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

> show sel atoms

> select #4/B:258

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

> select #4/B:258

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

> select #4/B:258-276

147 atoms, 146 bonds, 57 pseudobonds, 19 residues, 2 models selected  

> hide sel cartoons

Drag select of 16 atoms, 15 bonds  

> select #4/B:198

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

> select #4/B:182-198

137 atoms, 138 bonds, 54 pseudobonds, 17 residues, 2 models selected  

> show sel cartoons

> hide #6 models

Drag select of 577 atoms, 141 residues, 488 bonds  

> show sel surfaces

> hide sel surfaces

Drag select of 15 residues  

> hide sel cartoons

> delete contacts

Missing or invalid "atoms" argument: invalid atoms specifier  

> hide #5 target m

> show #5 target m

> hide #5 target m

> close #5

> close #6

> select #4/A:350

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

> select #4/B:237

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

> select #4/A:350

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

> select #4/B:237

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

> clashes #4/A:350 #4:237

17 clashes  

> close #5

> clashes #4/A:350&#4:237

No atoms match given atom specifier  

> clashes #4/A:350to #4:237

5 clashes  

> clashes #4/A to #4

Expected a keyword  

> clashes #4/A to #4/B

Expected a keyword  

> clashes #4/A to #4/B

Expected a keyword  
Drag select of 174 atoms, 33 residues, 147 bonds, 1 pseudobonds  

> select clear

Drag select of 93 atoms, 23 residues, 79 bonds  

> select #4/A:386

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

> select #4/A:385-386

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

> select #4/A:387-388

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

> select #4/A:387-474

670 atoms, 682 bonds, 88 residues, 1 model selected  

> select #4/A:386

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

> select #4/A:331-386

476 atoms, 482 bonds, 56 residues, 1 model selected  

> clashes #4/A:331-386to #4/B

376 clashes  

> select #4/B:182

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

> select #4/B:182-184

23 atoms, 23 bonds, 3 residues, 1 model selected  

> select #4/B:182-183

16 atoms, 16 bonds, 2 residues, 1 model selected  

> select #4/B:182-414

1838 atoms, 1868 bonds, 18 pseudobonds, 233 residues, 2 models selected  

> select #4/B:392

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

> select #4/B:390-392

18 atoms, 17 bonds, 3 residues, 1 model selected  

> select #4/B:366

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

> select #4/B:365-366

20 atoms, 19 bonds, 2 residues, 1 model selected  

> select #4/B:333-334

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select #4/B:331-334

27 atoms, 26 bonds, 4 residues, 1 model selected  

> select #4/B:319

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

> select #4/B:316-319

31 atoms, 31 bonds, 4 residues, 1 model selected  

> select #4/B:300

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

> select #4/B:297-300

31 atoms, 31 bonds, 4 residues, 1 model selected  

> select #4/B:223

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

> select #4/B:222

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

> select #4/B:182

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

> select #4/B:182-222

324 atoms, 328 bonds, 1 pseudobond, 41 residues, 2 models selected  

> select #4/B:222-223

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #4/B:222-229

72 atoms, 74 bonds, 8 residues, 1 model selected  

> select #4/B:182

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

> select #4/B:182-245

515 atoms, 523 bonds, 2 pseudobonds, 64 residues, 2 models selected  

> select #4/B:182

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

> select #4/B:182-276

751 atoms, 761 bonds, 5 pseudobonds, 95 residues, 2 models selected  

> close #5

> clashes #4/A:331-386to #4/B:182-276

93 clashes  
Undo failed, probably because structures have been modified.  
[Repeated 1 time(s)]

> clashes #4/Ato #4/B

376 clashes  

> select #4/B:351

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

> select #4/B:351

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

> select #4/B:345-351

57 atoms, 57 bonds, 7 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> select #4/B:344

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

> select #4/B:335-344

80 atoms, 79 bonds, 10 residues, 1 model selected  

> hide sel cartoons

> select clear

[Repeated 1 time(s)]

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> rock

> sotp

Unknown command: sotp  

> stop

> rock

> select #4/A:331-386

476 atoms, 482 bonds, 56 residues, 1 model selected  

> select #4/A:349

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

> select #4/A:349-350

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

> select #4/A:357

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

> select #4/A:357-358

20 atoms, 20 bonds, 2 residues, 1 model selected  

> select #4/A:337

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

> select #4/A:337-360

223 atoms, 228 bonds, 24 residues, 1 model selected  

> select #4/A:334

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

> select #4/A:334-374

362 atoms, 367 bonds, 41 residues, 1 model selected  

> stop

> view matrix models #4,1,0,0,5.7752,0,1,0,-33.399,0,0,1,15.219

> 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 "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

  

> ui mousemode right select

> select #4/A:374

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

> select #4/A:374

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

> select #4/A:371

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

> select #4/A:374

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

> select clear

> save
> C:/Users/Zuijderveltjl/Documents/LACDR/ASXL1/AlphaFold2/Interactions/RARA_ASXL1.cxs

> view

> ui mousemode right "next docked"

[Repeated 4 time(s)]

> ui mousemode right select

> ui mousemode right distance

> distance #4/A:356@OE2 #4/B:244@NZ

Distance between ASX1L:RARA #4/A GLU 356 OE2 and /B LYS 244 NZ: 1.981Å  

> distance #4/B:244@NZ #4/B:250@CG2

Distance between ASX1L:RARA #4/B LYS 244 NZ and THR 250 CG2: 7.450Å  

> ~distance #4/B:244@NZ #4/B:250@CG2

> distance #4/B:244@NZ #4/A:359@OH

Distance between ASX1L:RARA #4/B LYS 244 NZ and /A TYR 359 OH: 5.285Å  

> ~distance #4/B:244@NZ #4/A:359@OH

> distance #4/B:244@NZ #4/A:359@CD2

Distance between ASX1L:RARA #4/B LYS 244 NZ and /A TYR 359 CD2: 3.815Å  

> ~distance #4/B:244@NZ #4/A:359@CD2

> hide #6.1 models

> hide #!6 models

> close session

> open
> C:\Users\Zuijderveltjl\Documents\LACDR\ASXL1\AlphaFold2\Human\ASXL1_WT.pdb
> format pdb

ASXL1_WT.pdb title:  
Alphafold monomer V2.0 prediction for polycomb group protein ASXL1 (Q8IXJ9)
[more info...]  
  
Chain information for ASXL1_WT.pdb #1  
---  
Chain | Description | UniProt  
A | polycomb group protein ASXL1 | ASXL1_HUMAN 1-1541  
  

> select coils

Expected an objects specifier or a keyword  

> select coil

10312 atoms, 10505 bonds, 1385 residues, 1 model selected  

> hide

> delete

Missing or invalid "atoms" argument: empty atom specifier  

> delete

Missing or invalid "atoms" argument: empty atom specifier  

> delete se

Missing or invalid "atoms" argument: invalid atoms specifier  

> delete sel

> color sequential #1&helix palette cornflower:teal

> color sequential #1&strand palette salmon:hotpink

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> select /A:2

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

> select /A:2-86

366 atoms, 366 bonds, 7 pseudobonds, 45 residues, 2 models selected  

> select /A:2-62,86-292,307-1120,1537-1540

1124 atoms, 1122 bonds, 16 pseudobonds, 138 residues, 2 models selected  

> select /A:2-86

366 atoms, 366 bonds, 7 pseudobonds, 45 residues, 2 models selected  

> select /A:2-86

366 atoms, 366 bonds, 7 pseudobonds, 45 residues, 2 models selected  

> select /A:2-86

366 atoms, 366 bonds, 7 pseudobonds, 45 residues, 2 models selected  

> select /A:2-88

379 atoms, 379 bonds, 7 pseudobonds, 47 residues, 2 models selected  

> show sel cartoons

[Repeated 2 time(s)]

> show coil

> close session

> open
> C:\Users\Zuijderveltjl\Documents\LACDR\ASXL1\AlphaFold2\Human\ASXL1_WT.pdb
> format pdb

ASXL1_WT.pdb title:  
Alphafold monomer V2.0 prediction for polycomb group protein ASXL1 (Q8IXJ9)
[more info...]  
  
Chain information for ASXL1_WT.pdb #1  
---  
Chain | Description | UniProt  
A | polycomb group protein ASXL1 | ASXL1_HUMAN 1-1541  
  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> select
> /A:2-4,6-8,13-23,31-40,52-62,86-88,264-267,270-275,278-287,290-292,307-309,311-325,331-344,351-354,369-375,614-627,1066-1068,1106-1112,1118-1120,1537-1540

1124 atoms, 1122 bonds, 138 residues, 1 model selected  

> ui mousemode right select

> select clear

> select /A:3

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

> select clear

> select /A:3

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

> select /A:2

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

> select clear

[Repeated 2 time(s)]

> select /A:1

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

> select /A:3

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

> select /A:7

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

> select clear

[Repeated 2 time(s)]Drag select of 1 residues  

> select /A:92-93

21 atoms, 21 bonds, 2 residues, 1 model selected  

> select /A:92-253

1179 atoms, 1195 bonds, 162 residues, 1 model selected  

> delete sel

Drag select of 2 residues  

> select /A:378-379

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select /A:378-610

1818 atoms, 1859 bonds, 233 residues, 1 model selected  

> delete sel

Drag select of 2 residues  

> select /A:631

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

> select /A:631-1062

3162 atoms, 3227 bonds, 432 residues, 1 model selected  

> delete sel

> select
> /A:2-4,6-8,13-23,31-40,52-62,86-88,264-267,270-275,278-287,290-292,307-309,311-325,331-344,351-354,369-375,614-627,1066-1068,1106-1112,1118-1120,1537-1540

1124 atoms, 1122 bonds, 138 residues, 1 model selected  

> select clear

> select
> /A:2-4,6-8,13-23,31-40,52-62,86-88,264-267,270-275,278-287,290-292,307-309,311-325,331-344,351-354,369-375,614-627,1066-1068,1106-1112,1118-1120,1537-1540

1124 atoms, 1122 bonds, 138 residues, 1 model selected  

> select clear

Drag select of 5 residues  

> select clear

Drag select of 7 residues  

> select /A:1141-1142

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select /A:1141-1509

2727 atoms, 2792 bonds, 369 residues, 1 model selected  

> delete sel

> open "C:/Users/Zuijderveltjl/Documents/LACDR/ASXL1/AlphaFold2/Unpacked/BOS
> mutant/Trunc 573/Trunc573.pdb"

Chain information for Trunc573.pdb #2  
---  
Chain | Description  
A | No description available  
  

> select
> #1/A:2-4,6-8,13-23,31-40,52-62,86-88,264-267,270-275,278-287,290-292,307-309,311-325,331-344,351-354,369-375,614-627,1066-1068,1106-1112,1118-1120,1537-1540

1124 atoms, 1122 bonds, 138 residues, 1 model selected  

> select #1/A:2

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

> select #1/A:2-91

711 atoms, 723 bonds, 90 residues, 1 model selected  

> matchmaker #2:1-100 to #1:1-100

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker ASXL1_WT.pdb, chain A (#1) with Trunc573.pdb, chain A (#2),
sequence alignment score = 419.4  
RMSD between 78 pruned atom pairs is 0.548 angstroms; (across all 91 pairs:
3.029)  
  

> matchmaker #2:1-100 to #1:1-100, show true

Expected a keyword  

> matchmaker #2:1-100 to #1:1-100, show true

Expected a keyword  

> matchmaker #2:1-100 to #1:1-100, show=true

Invalid "to" argument: only initial part "#1:1-100" of atom specifier valid  

> matchmaker #2:1-100 to #1:1-100, show istrue

Expected a keyword  

> matchmaker #2:1-100 to #1:1-100, show is true

Expected a keyword  

> matchmaker #2:1-100 to #1:1-100 showAlignment true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker ASXL1_WT.pdb, chain A (#1) with Trunc573.pdb, chain A (#2),
sequence alignment score = 419.4  
Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: ASXL1_WT.pdb #1/A,
Trunc573.pdb #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 78 pruned atom pairs is 0.548 angstroms; (across all 91 pairs:
3.029)  
  

> select clear

> select #1/A:89

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

> select #1/A:89-91

29 atoms, 30 bonds, 3 residues, 1 model selected  

> close session

> open "C:\Users\Zuijderveltjl\Documents\LACDR\ASXL1\AlphaFold2\Unpacked\BOS
> mutant\Trunc 573\Trunc573.pdb" format pdb

Chain information for Trunc573.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open
> C:\Users\Zuijderveltjl\Documents\LACDR\ASXL1\AlphaFold2\Human\ASXL1_WT.pdb
> format pdb

ASXL1_WT.pdb title:  
Alphafold monomer V2.0 prediction for polycomb group protein ASXL1 (Q8IXJ9)
[more info...]  
  
Chain information for ASXL1_WT.pdb #2  
---  
Chain | Description | UniProt  
A | polycomb group protein ASXL1 | ASXL1_HUMAN 1-1541  
  

> matchmaker #2:1-85 to #1:1-85 showAlignment true

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Trunc573.pdb, chain A (#1) with ASXL1_WT.pdb, chain A (#2),
sequence alignment score = 392.6  
Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: Trunc573.pdb #1/A,
ASXL1_WT.pdb #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 72 pruned atom pairs is 0.558 angstroms; (across all 85 pairs:
3.130)  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> sequence chain #2/A

Alignment identifier is 2/A  

> select #1/A:87-88

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

> select #1/A:87-573

3767 atoms, 3838 bonds, 487 residues, 1 model selected  

> delete sel

> select #2/A:87-88

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

> select #2/A:87-1541

10922 atoms, 11152 bonds, 1455 residues, 1 model selected  

> delete sel

> ui tool show "Render By Attribute"

> color byattribute r:seq_rmsd target absc palette
> 0.0797467,blue:2,yellow:3,red noValueColor grey

1354 atoms, 172 residues, atom seq_rmsd range 0.0797 to 13.8  

> select clear

Drag select of 2 residues  

> select #2/A:3

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

> select clear

Drag select of 2 residues  
Drag select of 6 residues  
Drag select of 17 residues  

> select clear

> hide #1 models

Drag select of 35 residues  

> select clear

> color sequential palette cornflower:teal

> color sequential palette cornflower:salmon

> color sequential palette cornflower:white:hotpink

> select clear

Drag select of 1 residues  

> color blue

> color sel blue

> select clear

Drag select of 3 residues  

> select clear

Drag select of 1 residues  

> color sel red

> select clear

[Repeated 1 time(s)]

> set bgColor white

> lighting soft

> graphics silhouettes true

> lighting shadows true intensity 0.5

Drag select of 8 residues  

> select clear

[Repeated 1 time(s)]

> show #1 models

> hide #2 models

> ui tool show "Render By Attribute"

> 2dlabels

> color byattribute r:seq_rmsd target absc palette 0.5,blue:1,yellow:2,red
> noValueColor grey

1354 atoms, 172 residues, atom seq_rmsd range 0.0797 to 13.8  

> color byattribute r:seq_rmsd target absc palette 0.5,blue:1,yellow:2,red
> noValueColor grey

1354 atoms, 172 residues, atom seq_rmsd range 0.0797 to 13.8  

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> undo

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> ui mousemode right rotate

> ui mousemode right select

> select #1/A:85

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

> select clear

> show #2 models

> hide #1 models

Drag select of 1 residues  

> select clear

> show #1 models

> hide #2 models

> ui tool show "Render By Attribute"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 759, in _set_value_cb  
self._redraw_cb()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 643, in _redraw_cb  
filled_bins = self._bins(int(hist_width * filled_range / full_range))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\render_by_attr\tool.py", line 345, in <lambda>  
numpy.histogram(values, bins=num_bins, range=(min_val, max_val),
density=False)[0])  
File "<__array_function__ internals>", line 180, in histogram  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\numpy\lib\histograms.py", line 793, in histogram  
bin_edges, uniform_bins = _get_bin_edges(a, bins, range, weights)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\numpy\lib\histograms.py", line 424, in _get_bin_edges  
raise ValueError('`bins` must be positive, when an integer')  
ValueError: `bins` must be positive, when an integer  
  
ValueError: `bins` must be positive, when an integer  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\numpy\lib\histograms.py", line 424, in _get_bin_edges  
raise ValueError('`bins` must be positive, when an integer')  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 760, in _set_value_cb  
self._move_cur_marker(v)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 570, in _move_cur_marker  
self._active_markers._update_plot()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 1222, in _update_plot  
self._update_marker_coordinates()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 1207, in
_update_marker_coordinates  
x, y = self._scene_xy(m.xy)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 1090, in _scene_xy  
return self.histogram._scene_xy(abs_xy)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 512, in _scene_xy  
num_bins = len(self._bins)  
TypeError: object of type 'function' has no len()  
  
TypeError: object of type 'function' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 512, in _scene_xy  
num_bins = len(self._bins)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 179, in <lambda>  
if event.modifiers() & mod_key_info("shift")[0] else
self._select_marker_cb(event)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 718, in _select_marker_cb  
self._set_value_entry(self._abs_xy((event.scenePos().x(), 0))[0])  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
TypeError: object of type 'function' has no len()  
  
TypeError: object of type 'function' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 179, in <lambda>  
if event.modifiers() & mod_key_info("shift")[0] else
self._select_marker_cb(event)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 714, in _select_marker_cb  
self._set_sel_marker(marker, drag_start=event)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 743, in _set_sel_marker  
self._last_mouse_xy = self._abs_xy((drag_start.scenePos().x(),
drag_start.scenePos().y()))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
TypeError: object of type 'function' has no len()  
  
TypeError: object of type 'function' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 180, in <lambda>  
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 576, in _move_marker_cb  
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
TypeError: object of type 'function' has no len()  
  
TypeError: object of type 'function' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 180, in <lambda>  
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 576, in _move_marker_cb  
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
TypeError: object of type 'function' has no len()  
  
TypeError: object of type 'function' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 180, in <lambda>  
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 576, in _move_marker_cb  
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
TypeError: object of type 'function' has no len()  
  
TypeError: object of type 'function' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 180, in <lambda>  
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 576, in _move_marker_cb  
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
TypeError: object of type 'function' has no len()  
  
TypeError: object of type 'function' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 180, in <lambda>  
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 576, in _move_marker_cb  
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
TypeError: object of type 'function' has no len()  
  
TypeError: object of type 'function' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 180, in <lambda>  
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 576, in _move_marker_cb  
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
TypeError: object of type 'function' has no len()  
  
TypeError: object of type 'function' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 180, in <lambda>  
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 576, in _move_marker_cb  
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
TypeError: object of type 'function' has no len()  
  
TypeError: object of type 'function' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 180, in <lambda>  
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 576, in _move_marker_cb  
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
TypeError: object of type 'function' has no len()  
  
TypeError: object of type 'function' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 180, in <lambda>  
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 576, in _move_marker_cb  
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
TypeError: object of type 'function' has no len()  
  
TypeError: object of type 'function' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 180, in <lambda>  
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 576, in _move_marker_cb  
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
TypeError: object of type 'function' has no len()  
  
TypeError: object of type 'function' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 180, in <lambda>  
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 576, in _move_marker_cb  
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
TypeError: object of type 'function' has no len()  
  
TypeError: object of type 'function' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 180, in <lambda>  
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 576, in _move_marker_cb  
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
TypeError: object of type 'function' has no len()  
  
TypeError: object of type 'function' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 180, in <lambda>  
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 576, in _move_marker_cb  
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
TypeError: object of type 'function' has no len()  
  
TypeError: object of type 'function' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 180, in <lambda>  
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 576, in _move_marker_cb  
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
TypeError: object of type 'function' has no len()  
  
TypeError: object of type 'function' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 180, in <lambda>  
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 576, in _move_marker_cb  
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
TypeError: object of type 'function' has no len()  
  
TypeError: object of type 'function' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 180, in <lambda>  
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 576, in _move_marker_cb  
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
TypeError: object of type 'function' has no len()  
  
TypeError: object of type 'function' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 180, in <lambda>  
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 576, in _move_marker_cb  
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
TypeError: object of type 'function' has no len()  
  
TypeError: object of type 'function' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 180, in <lambda>  
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 576, in _move_marker_cb  
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
TypeError: object of type 'function' has no len()  
  
TypeError: object of type 'function' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 180, in <lambda>  
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 576, in _move_marker_cb  
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
TypeError: object of type 'function' has no len()  
  
TypeError: object of type 'function' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 180, in <lambda>  
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 576, in _move_marker_cb  
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
TypeError: object of type 'function' has no len()  
  
TypeError: object of type 'function' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 180, in <lambda>  
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 576, in _move_marker_cb  
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
TypeError: object of type 'function' has no len()  
  
TypeError: object of type 'function' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 180, in <lambda>  
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 576, in _move_marker_cb  
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
TypeError: object of type 'function' has no len()  
  
TypeError: object of type 'function' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 180, in <lambda>  
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 576, in _move_marker_cb  
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
TypeError: object of type 'function' has no len()  
  
TypeError: object of type 'function' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 180, in <lambda>  
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 576, in _move_marker_cb  
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
TypeError: object of type 'function' has no len()  
  
TypeError: object of type 'function' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 180, in <lambda>  
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 576, in _move_marker_cb  
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
TypeError: object of type 'function' has no len()  
  
TypeError: object of type 'function' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 180, in <lambda>  
self._hist_scene.mouseMoveEvent = lambda event: self._move_marker_cb(event) \  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 576, in _move_marker_cb  
mouse_xy = self._abs_xy((event.scenePos().x(), event.scenePos().y()))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
TypeError: object of type 'function' has no len()  
  
TypeError: object of type 'function' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\histogram.py", line 441, in _abs_xy  
num_bins = len(self._bins)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 31.0.101.4091
OpenGL renderer: Intel(R) UHD Graphics
OpenGL vendor: Intel

Python: 3.9.11
Locale: nl_NL.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: HP
Model: HP EliteBook 630 13 inch G9 Notebook PC
OS: Microsoft Windows 10 Enterprise (Build 19045)
Memory: 16,794,439,680
MaxProcessMemory: 137,438,953,344
CPU: 12 12th Gen Intel(R) Core(TM) i5-1235U
OSLanguage: en-GB

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    comtypes: 1.1.14
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pywin32: 305
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    WMI: 1.5.1
    zipp: 3.15.0