ISOLDE: Can't install package: invalid requirement specified

[ichcharisma@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
Every time i try to install ISOLDE through Tools > More Tools, the loading process below the windows never finished even the .whl file in my finder shows complete download. So no pop up for installing ISOLDE

Log:
> open 7u0n

7u0n title:  
Crystal structure of chimeric ο RBD (strain BA.1) complexed with human ACE2
[more info...]  
  
Chain information for 7u0n #1  
---  
Chain | Description | UniProt  
A B | Angiotensin-converting enzyme 2 | ACE2_HUMAN  
E F | Spike protein S1 |  
  
Non-standard residues in 7u0n #1  
---  
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)  
CL — chloride ion  
EDO — 1,2-ethanediol (ethylene glycol)  
MG — magnesium ion  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
ZN — zinc ion  
  
7u0n mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> sym #1 assembly 1 copies true

> close #1

> view

> delete ~protein

> color bychaij

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

> color bychain

> viewe top

Unknown command: viewe top  

> view

> view matrix

view matrix camera 1,0,0,16.215,0,1,0,-1.4103,0,0,1,446.16  
view matrix models
#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.1.2,1,0,0,0,0,1,0,0,0,0,1,0  
  

> turn y 90

[Repeated 3 time(s)]

> turn x 90

[Repeated 3 time(s)]

> turn z 90

[Repeated 2 time(s)]

> view

> turn z 90

> \

Unknown command: \  

> \

Unknown command: \  

> turn z 90

> turn y 90

[Repeated 1 time(s)]

> select /a

4862 atoms, 5002 bonds, 596 residues, 1 model selected  

> select /b

Nothing selected  

> select /c

Nothing selected  

> select /e

1500 atoms, 1546 bonds, 1 pseudobond, 188 residues, 2 models selected  

> select zone /e 10

Selected 412 atoms  

> hbonds sel restrict /e intraMol true log true reveal true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	2.1 7u0n
    
    11 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /A SER 19 OG    /E ALA 475 O    no hydrogen  3.403  N/A
    /A HIS 34 NE2   /E SER 494 O    no hydrogen  3.211  N/A
    /A TYR 41 OH    /E THR 500 OG1  no hydrogen  2.491  N/A
    /A TYR 83 OH    /E ASN 487 OD1  no hydrogen  2.332  N/A
    /E ARG 439 NH2  /A GLU 329 OE2  no hydrogen  3.369  N/A
    /E TYR 449 OH   /A ASP 38 OD1   no hydrogen  3.373  N/A
    /E TYR 449 OH   /A ASP 38 OD2   no hydrogen  3.173  N/A
    /E ASN 487 ND2  /A GLN 24 OE1   no hydrogen  2.960  N/A
    /E SER 496 OG   /A ASP 38 OD1   no hydrogen  2.508  N/A
    /E THR 500 OG1  /A TYR 41 OH    no hydrogen  2.491  N/A
    /E GLY 502 N    /A LYS 353 O    no hydrogen  3.175  N/A
    

  
11 hydrogen bonds found  

> surface /e color tan

> lighting soft

> select fro name zone10 sel

Expected an objects specifier or a keyword  

> name frozen zone10 sel

> select clear

> label hbond

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> label hyd

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> label hydrogen bonds

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> label #2.1.3

> label #2.1.3 height 5 offset 1,1,1

> label #2.1.3 height 1 offset 1,1,1

> select /a

4862 atoms, 5002 bonds, 596 residues, 1 model selected  

> hide sel target c

> color sel byelement

Drag select of 85 atoms, 79 bonds  

> hide sel target a

Drag select of 23 atoms, 22 bonds  
Drag select of 25 atoms, 23 bonds  
Drag select of 8 atoms, 7 bonds  
Drag select of 18 atoms, 16 bonds  
Drag select of 8 atoms, 7 bonds  

> hide sel target a

> select up

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

> select up

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

> hide sel target a

> view

> label #2.1.3 height 0.1 offset 1,1,1

> label #2.1.3 height 0.5 offset 1,1,1

> select /e

1500 atoms, 1546 bonds, 1 pseudobond, 188 residues, 2 models selected  

> select /a

4862 atoms, 5002 bonds, 596 residues, 1 model selected  

> select /e

1500 atoms, 1546 bonds, 1 pseudobond, 188 residues, 2 models selected  

> color sel tan target c

> select clear

> select /e

1500 atoms, 1546 bonds, 1 pseudobond, 188 residues, 2 models selected  

> select /e:439,449,487,496,500,502,475,494,500,487

59 atoms, 52 bonds, 8 residues, 1 model selected  

> color sel orange

> select clear

> lighting simple

> lighting soft

> lighting full

> lighting soft

> show /e

> show /a target c

> select residues true sequence IEEQAKTFLDKFNHEAEDLF

171 atoms, 174 bonds, 20 residues, 1 model selected  

> select residues true sequence

Missing "sequence" keyword's argument  

> AGDKWSAFLKE

Unknown command: AGDKWSAFLKE  

> AGDKWSAFLKE

Unknown command: AGDKWSAFLKE  

> select clear

> select residues true sequence

Missing "sequence" keyword's argument  

> AGDKWSAFLKE

Unknown command: AGDKWSAFLKE  

> select residues true sequence

Missing "sequence" keyword's argument  

> AGDKWSAFLKE

Unknown command: AGDKWSAFLKE  

> select residues true sequence AGDKWSAFLKE

88 atoms, 90 bonds, 11 residues, 1 model selected  
Alignment identifier is 2.1/A  

> select residues true sequence AGDKWSAFLKE

88 atoms, 90 bonds, 11 residues, 1 model selected  

> select residues true sequence AGDKWSAFLKE

88 atoms, 90 bonds, 11 residues, 1 model selected  

> select
> /A:20-52,55-88,90-101,103-130,146-155,157-195,198-208,218-252,265-267,275-283,293-300,303-318,324-331,336-340,365-393,399-422,431-446,449-466,469-484,499-508,513-533,538-542,547-559,565-575,581-602

3611 atoms, 3686 bonds, 436 residues, 1 model selected  

> select clear

>

Incomplete command: sequence  

> show

Unknown command: sequence show  

> sequence chain /e

Alignment identifier is 2.1/E  

> select /A:65-66

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

> select /A:65-74

79 atoms, 81 bonds, 10 residues, 1 model selected  

> select /E:455

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

> select /E:455-456

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

> select /A:65

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

> select /A:65-71

51 atoms, 52 bonds, 7 residues, 1 model selected  

> select /E:455

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

> select /E:455-458

39 atoms, 39 bonds, 4 residues, 1 model selected  

> select residues true sequence AGDKWSAFLKE

88 atoms, 90 bonds, 11 residues, 1 model selected  

> hide #!2 models

> open 6m17

Summary of feedback from opening 6m17 fetched from pdb  
---  
note | Fetching compressed mmCIF 6m17 from
http://files.rcsb.org/download/6m17.cif  
  
6m17 title:  
The 2019-nCoV RBD/ACE2-B0AT1 complex [more info...]  
  
Chain information for 6m17 #1  
---  
Chain | Description | UniProt  
A C | Sodium-dependent neutral amino acid transporter B(0)AT1 | S6A19_HUMAN  
B D | Angiotensin-converting enzyme 2 | ACE2_HUMAN  
E F | Spike protein S1 | SPIKE_SARS2  
  
Non-standard residues in 6m17 #1  
---  
LEU — leucine  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
ZN — zinc ion  
  

> view

> sym #1 assembly 1 copy t

Expected a keyword  

> sym #1 assembly 1

> hide #!3.1 models

> show #!3.1 models

> hide #!3.1 models

> show #!3.1 models

> delete ~protein

> hide #1 target a

> hide #3 target a

> show #3 target c

> select residues true sequence AGDKWSAFLKE

440 atoms, 450 bonds, 55 residues, 3 models selected  

> sequence chain #3/b

Alignment identifier is 3.1/B  

> select #1/B:21-768

6089 atoms, 6255 bonds, 748 residues, 1 model selected  

> select #1/B:21-768

6089 atoms, 6255 bonds, 748 residues, 1 model selected  

> select #1/D:21-768

6089 atoms, 6255 bonds, 748 residues, 1 model selected  

> close #1

> select #3.1/B:65-66

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

> select #3.1/B:65-74

79 atoms, 81 bonds, 10 residues, 1 model selected  

> select #3.1/B:22

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

> select #3.1/B:22-29

67 atoms, 67 bonds, 8 residues, 1 model selected  

> hide #!3 models

> show #!2 models

> view

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/ich/Desktop/movie1.mp4

Movie saved to /Users/ich/Desktop/movie1.mp4  
  

> close #3

> view

[Repeated 1 time(s)]

> hide /e target c

> view

> ui mousemode right select

Drag select of 263 residues  

> select up

3122 atoms, 3205 bonds, 378 residues, 1 model selected  

> select up

4862 atoms, 5002 bonds, 596 residues, 1 model selected  

> hide sel target c

> view

> select clear

> select /E:415@O

1 atom, 1 residue, 1 model selected  

> select up

7 atoms, 6 bonds, 1 residue, 2 models selected  

> select up

32 atoms, 32 bonds, 5 residues, 2 models selected  

> select up

1500 atoms, 1546 bonds, 188 residues, 2 models selected  

> select up

6362 atoms, 6548 bonds, 784 residues, 2 models selected  

> select down

1500 atoms, 1546 bonds, 188 residues, 2 models selected  

> hide sel target s

> select clear

> select /E:509@NH1

1 atom, 1 residue, 1 model selected  

> select up

11 atoms, 10 bonds, 1 residue, 2 models selected  

> select up

93 atoms, 95 bonds, 11 residues, 2 models selected  

> select up

1500 atoms, 1546 bonds, 188 residues, 2 models selected  

> color sel dark red

> select clear

> lighting full

> select up

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

> select up

7 atoms, 6 bonds, 1 residue, 2 models selected  

> color sel byelement

> select up

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

> select up

11 atoms, 10 bonds, 1 residue, 2 models selected  

> color sel by chain

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

> color sel byelement

> select up

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

> select up

4 atoms, 3 bonds, 1 residue, 2 models selected  

> select up

25 atoms, 25 bonds, 4 residues, 2 models selected  

> color sel byelement

> view

> select up

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

> select up

8 atoms, 7 bonds, 1 residue, 2 models selected  

> color sel byelement

> select up

2 atoms, 1 bond, 2 residues, 1 model selected  

> select up

9 atoms, 8 bonds, 2 residues, 2 models selected  

> color sel byelement

> select /E:477@CB

1 atom, 1 residue, 1 model selected  

> select up

6 atoms, 5 bonds, 1 residue, 2 models selected  

> select up

82 atoms, 83 bonds, 13 residues, 2 models selected  

> select up

1500 atoms, 1546 bonds, 188 residues, 2 models selected  

> show sel target s

> surface sel color tan

> select clear

> select /E:477@CB

1 atom, 1 residue, 1 model selected  

> select up

6 atoms, 5 bonds, 1 residue, 2 models selected  

> select up

82 atoms, 83 bonds, 13 residues, 2 models selected  

> select up

1500 atoms, 1546 bonds, 188 residues, 2 models selected  

> transparency surf

Missing or invalid "percent" argument: Expected a number  

> transparency surf 50

Missing or invalid "percent" argument: Expected a number  

> transparency sel 50

> view

> sill t

Unknown command: sill t  

> transparency sel 80

> set bgColor white

> surface sel color dark green

> transparency sel 80

> graphics silhouettes true

> lighting soft

> open open 6m17

'open' has no suffix  

> open 6m17

6m17 title:  
The 2019-nCoV RBD/ACE2-B0AT1 complex [more info...]  
  
Chain information for 6m17 #1  
---  
Chain | Description | UniProt  
A C | Sodium-dependent neutral amino acid transporter B(0)AT1 | S6A19_HUMAN  
B D | Angiotensin-converting enzyme 2 | ACE2_HUMAN  
E F | Spike protein S1 | SPIKE_SARS2  
  
Non-standard residues in 6m17 #1  
---  
LEU — leucine  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
ZN — zinc ion  
  

> hide #!2 models

> view

> delete ~protein

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/ich/Desktop/movie2.mp4

Movie saved to /Users/ich/Desktop/movie2.mp4  
  

> color #1 bychain

> hide #1 target a

> show #1 target c

> select #1/e,f

2924 atoms, 3012 bonds, 366 residues, 1 model selected  

> select #1/a,c

9598 atoms, 9884 bonds, 1210 residues, 1 model selected  

> delete sel

> select #1/d,f

7551 atoms, 7761 bonds, 931 residues, 1 model selected  

> delete sel

> view

> select #1/e

1462 atoms, 1506 bonds, 183 residues, 1 model selected  

> show sel target s

> color list

1 custom color: ocean

.  
248 builtin colors: alice blue

, aliceblue

, antique white

, antiquewhite

, aqua

, aquamarine

, azure

, beige

, bisque

, black

, blanched almond

, blanchedalmond

, blue

, blue violet

, blueviolet

, brown

, burly wood

, burlywood

, cadet blue

, cadetblue

, chartreuse

, chocolate

, coral

, cornflower blue

, cornflowerblue

, cornsilk

, crimson

, cyan

, dark blue

, dark cyan

, dark goldenrod

, dark gray

, dark green

, dark grey

, dark khaki

, dark magenta

, dark olive green

, dark orange

, dark orchid

, dark red

, dark salmon

, dark sea green

, dark seagreen

, dark slate blue

, dark slate gray

, dark slate grey

, dark turquoise

, dark violet

, darkblue

, darkcyan

, darkgoldenrod

, darkgray

, darkgreen

, darkgrey

, darkkhaki

, darkmagenta

, darkolivegreen

, darkorange

, darkorchid

, darkred

, darksalmon

, darkseagreen

, darkslateblue

, darkslategray

, darkslategrey

, darkturquoise

, darkviolet

, deep pink

, deep sky blue

, deep skyblue

, deeppink

, deepskyblue

, dim gray

, dim grey

, dimgray

, dimgrey

, dodger blue

, dodgerblue

, fire brick

, firebrick

, floral white

, floralwhite

, forest green

, forestgreen

, fuchsia

, gainsboro

, ghost white

, ghostwhite

, gold

, goldenrod

, gray

, green

, green yellow

, greenyellow

, grey

, honeydew

, hot pink

, hotpink

, indian red

, indianred

, indigo

, ivory

, khaki

, lavender

, lavender blush

, lavenderblush

, lawn green

, lawngreen

, lemon chiffon

, lemonchiffon

, light blue

, light coral

, light cyan

, light goldenrod yellow

, light gray

, light green

, light grey

, light pink

, light salmon

, light sea green

, light seagreen

, light sky blue

, light skyblue

, light slate gray

, light slate grey

, light steel blue

, light yellow

, lightblue

, lightcoral

, lightcyan

, lightgoldenrodyellow

, lightgray

, lightgreen

, lightgrey

, lightpink

, lightsalmon

, lightseagreen

, lightskyblue

, lightslategray

, lightslategrey

, lightsteelblue

, lightyellow

, lime

, lime green

, limegreen

, linen

, magenta

, maroon

, medium aquamarine

, medium blue

, medium orchid

, medium purple

, medium sea green

, medium seagreen

, medium slate blue

, medium spring green

, medium turquoise

, medium violet red

, mediumaquamarine

, mediumblue

, mediumorchid

, mediumpurple

, mediumseagreen

, mediumslateblue

, mediumspringgreen

, mediumturquoise

, mediumvioletred

, midnight blue

, midnightblue

, mint cream

, mintcream

, misty rose

, mistyrose

, moccasin

, navajo white

, navajowhite

, navy

, old lace

, oldlace

, olive

, olive drab

, olivedrab

, orange

, orange red

, orangered

, orchid

, pale goldenrod

, pale green

, pale turquoise

, pale violet red

, palegoldenrod

, palegreen

, paleturquoise

, palevioletred

, papaya whip

, papayawhip

, peach puff

, peachpuff

, peru

, pink

, plum

, powder blue

, powderblue

, purple

, rebecca purple

, rebeccapurple

, red

, rosy brown

, rosybrown

, royal blue

, royalblue

, saddle brown

, saddlebrown

, salmon

, sandy brown

, sandybrown

, sea green

, seagreen

, seashell

, sienna

, silver

, sky blue

, skyblue

, slate blue

, slate gray

, slate grey

, slateblue

, slategray

, slategrey

, snow

, spring green

, springgreen

, steel blue

, steelblue

, tan

, teal

, thistle

, tomato

, transparent

, turquoise

, violet

, wheat

, white

, white smoke

, whitesmoke

, yellow

, yellow green

, and yellowgreen

.  

> surface /e color tan transparency 80

> select clear

> select zone /b 10

Selected 362 atoms  

> hbonds sel restrict /b intraMol true reveal true log true label 2

Expected a keyword  

> hbonds sel restrict /b intraMol true reveal true log true showDist true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 6m17
    
    9 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    6m17 #1/B TYR 83 OH    6m17 #1/E ASN 487 OD1  no hydrogen  2.908  N/A
    6m17 #1/B LYS 353 NZ   6m17 #1/E GLY 496 O    no hydrogen  3.107  N/A
    6m17 #1/B LYS 353 NZ   6m17 #1/E ASN 501 OD1  no hydrogen  3.008  N/A
    6m17 #1/B ARG 357 NH1  6m17 #1/E THR 500 OG1  no hydrogen  2.577  N/A
    6m17 #1/E LYS 417 NZ   6m17 #1/B ASP 30 OD1   no hydrogen  3.085  N/A
    6m17 #1/E LYS 417 NZ   6m17 #1/B ASP 30 OD2   no hydrogen  2.921  N/A
    6m17 #1/E TYR 449 OH   6m17 #1/B ASP 38 OD1   no hydrogen  2.989  N/A
    6m17 #1/E GLN 498 NE2  6m17 #1/B GLN 42 OE1   no hydrogen  2.734  N/A
    6m17 #1/E THR 500 OG1  6m17 #1/B ASP 355 OD2  no hydrogen  3.101  N/A
    

  
9 hydrogen bonds found  

> style #1 stick

Changed 7551 atom styles  

> color #2.1.3 black models

> color #2.1.3 #00fdffff models

> color #1.3.1 black models

> color #1.3.1 #424242ff models

> color #1.3.1 #919191ff models

> color #1.3.1 #797979ff models

> color #1.3.1 #424242ff models

> label #1.3.1 height 0.5 offset 1,1,1

> select clear

> select add #1.3

9 pseudobonds, 2 models selected  

> select subtract #1.3

Nothing selected  

> select #1/E:487@OD1

1 atom, 1 residue, 1 model selected  

> select #1/E:487@OD1

1 atom, 1 residue, 1 model selected  

> select clear

> close #2

> select residues true sequence

Missing "sequence" keyword's argument  

> IEEQAKTFLDKFNHEAEDLF

Unknown command: IEEQAKTFLDKFNHEAEDLF  

> select residues true sequence IEEQAKTFLDKFNHEAEDLF

171 atoms, 174 bonds, 20 residues, 1 model selected  

> color

> color modify sel saturation 60

[Repeated 1 time(s)]

> color modify sel saturation -60

> color modify sel saturation 60

> undo

[Repeated 3 time(s)]

> color modify sel lightness 50

> color modify sel lightness -50

> color modify sel lightness 10

> color modify sel lightness -10

> color modify sel lightness -1

> color modify sel contrast 50

> color modify sel contrast 0

> color modify sel contrast 100

> color modify sel saturation 10

> color modify sel saturation 30

> color modify sel saturation 70

> color modify sel saturation 100

> color sel green sat 40

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

> color sel lightgreen

> select residues true sequence

Missing "sequence" keyword's argument  

> AGDKWSAFLKE

Unknown command: AGDKWSAFLKE  

> AGDKWSAFLKE

Unknown command: AGDKWSAFLKE  

> select residues true sequence AGDKWSAFLKE

88 atoms, 90 bonds, 11 residues, 1 model selected  

> color sel softgreen

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

> color sel darkgreen

> select clear

> select residues true sequence AGDKWSAFLKE

88 atoms, 90 bonds, 11 residues, 1 model selected  

> name frozen f1 sel

> select residues true sequence IEEQAKTFLDKFNHEAEDLF

171 atoms, 174 bonds, 20 residues, 1 model selected  

> name frozen f2 sel

> select /e

1462 atoms, 1506 bonds, 183 residues, 1 model selected  

> select /b

6089 atoms, 6255 bonds, 748 residues, 1 model selected  

> select subtract f1,f2

Expected an objects specifier or a keyword  

> select subtract f1 & f2

6089 atoms, 6255 bonds, 748 residues, 1 model selected  

> hide sel target c

> select f1 & f2

Nothing selected  

> show sel target c

> show f1 target c

> show f2 target c

> view

> select clear

> sill f

Unknown command: sill f  

> sil f

Unknown command: sil f  

> sil

Unknown command: sil  

> silh

Unknown command: silh  

> graphics silhouettes false

> sil

Unknown command: sil  

> graphics silhouettes 0.01

Expected true or false or a keyword  

> graphics silhouettes color grey

> graphics silhouettes #1 col grey

Expected true or false or a keyword  

> graphics silhouettes true

> graphics silhouettes width 0.5

> graphics silhouettes width 1

> label

> select clear

> select up

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

> select up

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

> select /B:355@CB

1 atom, 1 residue, 1 model selected  

> select clear

> sequence chain /b

Alignment identifier is 1/B  

> select /b

6089 atoms, 6255 bonds, 748 residues, 1 model selected  

> select clear

> label #1.3.1 height 3

> label #1.3.1 height 10

> label #1.3

> label #1.3 color dark grey

> label #1.3 color black

> label #1.3 color black size 10

> label #1.3 color black height 10

> label #1.3 color black size 48 height 1

> label #1.3 color black size 48 height 0.1

> label #1.3 color black size 48 height 0.5

> select /b

6089 atoms, 6255 bonds, 748 residues, 1 model selected  

> select /b:21-40

171 atoms, 174 bonds, 20 residues, 1 model selected  

> color list

1 custom color: ocean

.  
248 builtin colors: alice blue

, aliceblue

, antique white

, antiquewhite

, aqua

, aquamarine

, azure

, beige

, bisque

, black

, blanched almond

, blanchedalmond

, blue

, blue violet

, blueviolet

, brown

, burly wood

, burlywood

, cadet blue

, cadetblue

, chartreuse

, chocolate

, coral

, cornflower blue

, cornflowerblue

, cornsilk

, crimson

, cyan

, dark blue

, dark cyan

, dark goldenrod

, dark gray

, dark green

, dark grey

, dark khaki

, dark magenta

, dark olive green

, dark orange

, dark orchid

, dark red

, dark salmon

, dark sea green

, dark seagreen

, dark slate blue

, dark slate gray

, dark slate grey

, dark turquoise

, dark violet

, darkblue

, darkcyan

, darkgoldenrod

, darkgray

, darkgreen

, darkgrey

, darkkhaki

, darkmagenta

, darkolivegreen

, darkorange

, darkorchid

, darkred

, darksalmon

, darkseagreen

, darkslateblue

, darkslategray

, darkslategrey

, darkturquoise

, darkviolet

, deep pink

, deep sky blue

, deep skyblue

, deeppink

, deepskyblue

, dim gray

, dim grey

, dimgray

, dimgrey

, dodger blue

, dodgerblue

, fire brick

, firebrick

, floral white

, floralwhite

, forest green

, forestgreen

, fuchsia

, gainsboro

, ghost white

, ghostwhite

, gold

, goldenrod

, gray

, green

, green yellow

, greenyellow

, grey

, honeydew

, hot pink

, hotpink

, indian red

, indianred

, indigo

, ivory

, khaki

, lavender

, lavender blush

, lavenderblush

, lawn green

, lawngreen

, lemon chiffon

, lemonchiffon

, light blue

, light coral

, light cyan

, light goldenrod yellow

, light gray

, light green

, light grey

, light pink

, light salmon

, light sea green

, light seagreen

, light sky blue

, light skyblue

, light slate gray

, light slate grey

, light steel blue

, light yellow

, lightblue

, lightcoral

, lightcyan

, lightgoldenrodyellow

, lightgray

, lightgreen

, lightgrey

, lightpink

, lightsalmon

, lightseagreen

, lightskyblue

, lightslategray

, lightslategrey

, lightsteelblue

, lightyellow

, lime

, lime green

, limegreen

, linen

, magenta

, maroon

, medium aquamarine

, medium blue

, medium orchid

, medium purple

, medium sea green

, medium seagreen

, medium slate blue

, medium spring green

, medium turquoise

, medium violet red

, mediumaquamarine

, mediumblue

, mediumorchid

, mediumpurple

, mediumseagreen

, mediumslateblue

, mediumspringgreen

, mediumturquoise

, mediumvioletred

, midnight blue

, midnightblue

, mint cream

, mintcream

, misty rose

, mistyrose

, moccasin

, navajo white

, navajowhite

, navy

, old lace

, oldlace

, olive

, olive drab

, olivedrab

, orange

, orange red

, orangered

, orchid

, pale goldenrod

, pale green

, pale turquoise

, pale violet red

, palegoldenrod

, palegreen

, paleturquoise

, palevioletred

, papaya whip

, papayawhip

, peach puff

, peachpuff

, peru

, pink

, plum

, powder blue

, powderblue

, purple

, rebecca purple

, rebeccapurple

, red

, rosy brown

, rosybrown

, royal blue

, royalblue

, saddle brown

, saddlebrown

, salmon

, sandy brown

, sandybrown

, sea green

, seagreen

, seashell

, sienna

, silver

, sky blue

, skyblue

, slate blue

, slate gray

, slate grey

, slateblue

, slategray

, slategrey

, snow

, spring green

, springgreen

, steel blue

, steelblue

, tan

, teal

, thistle

, tomato

, transparent

, turquoise

, violet

, wheat

, white

, white smoke

, whitesmoke

, yellow

, yellow green

, and yellowgreen

.  

> color sel sesagreen

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

> color sel seagreen

> select /b:65-75

88 atoms, 90 bonds, 11 residues, 1 model selected  

> select /e:417,453,458

30 atoms, 28 bonds, 3 residues, 1 model selected  

> show sel target a

> color modify saturation 100

> redo

> undo

> suurf /b col tan trans 80

Unknown command: suurf /b col tan trans 80  

> surface /b color tan transparency 80

> delete /b targ s

Expected a keyword  

> surface /b f

Expected a keyword  

> surface hidePatches /b

> surface /e color tan transparency 80

> select clear

> select /B:355@OD2

1 atom, 1 residue, 1 model selected  

> select add /B:355@CA

2 atoms, 2 bonds, 1 residue, 2 models selected  

> select clear

> select add /B:42@CG

1 atom, 2 bonds, 1 residue, 1 model selected  

> select clear

> select add /B:355@OD2

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

> select add /E:449@CD1

2 atoms, 3 bonds, 2 residues, 2 models selected  

> select subtract /E:449@CD1

1 atom, 3 bonds, 1 residue, 3 models selected  

> select add /E:417@CE

2 atoms, 7 bonds, 2 residues, 2 models selected  

> select subtract /E:417@CE

1 atom, 7 bonds, 1 residue, 3 models selected  

> select add /E:453@OH

2 atoms, 8 bonds, 2 residues, 2 models selected  

> select subtract /E:453@OH

1 atom, 8 bonds, 1 residue, 3 models selected  

> color sel byhetero

> select clear

> select up

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

> select up

9 atoms, 8 bonds, 1 residue, 2 models selected  

> color sel byhetero

> select add /B:353@NZ

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

> select add /B:353@CE

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

> select add /B:353@CG

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

> select add /E:505@CD2

13 atoms, 13 bonds, 3 residues, 2 models selected  

> select add /B:353@CB

14 atoms, 13 bonds, 3 residues, 3 models selected  

> select subtract /E:505@CD2

13 atoms, 13 bonds, 2 residues, 3 models selected  

> select add /B:353@CA

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

> color sel byhetero

> select up

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

> select up

11 atoms, 10 bonds, 1 residue, 2 models selected  

> select up

13 atoms, 11 bonds, 2 residues, 2 models selected  

> select up

19 atoms, 17 bonds, 2 residues, 2 models selected  

> select up

21 atoms, 18 bonds, 3 residues, 2 models selected  

> select up

27 atoms, 24 bonds, 3 residues, 2 models selected  

> select up

29 atoms, 25 bonds, 4 residues, 2 models selected  

> select up

39 atoms, 36 bonds, 4 residues, 2 models selected  

> color sel byhetero

> select clear

> select add /E:449@CZ

1 atom, 1 residue, 1 model selected  

> select /E:449@CD2

1 atom, 1 residue, 1 model selected  

> select /E:449@CD2

1 atom, 1 residue, 1 model selected  

> select clear

> hide /e target s

> select up

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

> select up

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select up

18 atoms, 15 bonds, 3 residues, 2 models selected  

> select up

28 atoms, 26 bonds, 3 residues, 2 models selected  

> select up

34 atoms, 29 bonds, 6 residues, 2 models selected  

> select up

53 atoms, 49 bonds, 6 residues, 2 models selected  

> select up

57 atoms, 51 bonds, 8 residues, 2 models selected  

> select up

74 atoms, 69 bonds, 8 residues, 2 models selected  

> color sel byhetero

> label sel

> label sel height 0.5 offset 1,1,1

> select clear

> select add #1.3.1

1 model selected  

> select subtract #1.3.1

Nothing selected  

> select add #1.3

9 pseudobonds, 2 models selected  

> label sel color darkblue

> select clear

> label sel color darkblue height 0.3 offset 1,1,1

> select add #1.3

9 pseudobonds, 2 models selected  

> label sel color darkblue height 0.3 offset 1,1,1

> select clear

> surface showPatches /e

> surface /e color tan transparency 80

> select clear

> ui tool show Registration

Window position QRect(0,1010 575x313) outside any known screen, using primary
screen  

QDockWidget failed to find relevant screen info. screenFrom:
QScreen(0x60000171fb00, name="LG HDR WQHD") screenTo: QScreen(0x60000171fb00,
name="LG HDR WQHD") wdgScreen: QScreen(0x60000171fb00, name="LG HDR WQHD")
orgWdgScreen QScreen(0x0)  

[Repeated 61 time(s)]

> ui tool show Updates

Errors may have occurred when running pip:  

pip standard error:  
\---  
  
[notice] A new release of pip available: 22.2.2 -> 23.0  
[notice] To update, run: /Applications/ChimeraX.app/Contents/MacOS/ChimeraX -m
pip install --upgrade pip  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Collecting ChimeraX-AddH==2.1.3  
Using cached
https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxaddh/releases/2.1.3/ChimeraX_AddH-2.1.3-py3-none-
any.whl (30 kB)  
Collecting ChimeraX-HKCage==1.3  
Using cached
https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxhkcage/releases/1.3/ChimeraX_HKCage-1.3-py3-none-
any.whl (8.4 kB)  
Installing collected packages: ChimeraX-HKCage, ChimeraX-AddH  
Successfully installed ChimeraX-AddH-2.1.3 ChimeraX-HKCage-1.3  
\---  

Successfully installed ChimeraX-AddH-2.1.3 ChimeraX-HKCage-1.3  
Installed ChimeraX-AddH (2.1.3)  
Installed ChimeraX-HKCage (1.3)  

> toolshed show

Downloading bundle ChimeraX_ISOLDE-1.5-cp39-cp39-macosx_10_13_universal2.whl  
[Repeated 1 time(s)]

> pip install

Can't possibly install an unspecified package.  

> pip install
> /Users/ich/Downloads/ChimeraX_ISOLDE-1.5-cp39-cp39-macosx_10_13_universal2.whl

Can't install package: invalid requirement specified.  

> ui tool show Shell

Downloading bundle ChimeraX_StarMap-1.1.70-py3-none-any.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
  
[notice] A new release of pip available: 22.2.2 -> 23.0  
[notice] To update, run: /Applications/ChimeraX.app/Contents/MacOS/ChimeraX -m
pip install --upgrade pip  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing /Users/ich/Downloads/ChimeraX_StarMap-1.1.70-py3-none-any.whl  
Requirement already satisfied: ChimeraX-Core>=1.4 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-StarMap==1.1.70) (1.5)  
Requirement already satisfied: pyparsing in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-StarMap==1.1.70) (3.0.9)  
Collecting pyqtgraph  
Downloading pyqtgraph-0.13.1-py3-none-any.whl (966 kB)  
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 966.1/966.1 kB 1.7 MB/s eta 0:00:00  
Requirement already satisfied: numpy>=1.20.0 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from pyqtgraph->ChimeraX-StarMap==1.1.70) (1.23.1)  
Installing collected packages: pyqtgraph, ChimeraX-StarMap  
Successfully installed ChimeraX-StarMap-1.1.70 pyqtgraph-0.13.1  
\---  

Successfully installed ChimeraX-StarMap-1.1.70 pyqtgraph-0.13.1  
Installed ChimeraX-StarMap (1.1.70)  

> open
> /Users/ich/Downloads/ChimeraX_ISOLDE-1.5-cp39-cp39-macosx_10_13_universal2.whl

Unrecognized file suffix '.whl'  

> open
> /Users/ich/Downloads/ChimeraX_ISOLDE-1.5-cp39-cp39-macosx_10_13_universal2.whl

Unrecognized file suffix '.whl'  
Downloading bundle ChimeraX_ISOLDE-1.5-cp39-cp39-macosx_10_13_universal2.whl  
[Repeated 3 time(s)]

> pip install
> /Users/ich/Downloads/ChimeraX_ISOLDE-1.5-cp39-cp39-macosx_10_13_universal2.whl

Can't install package: invalid requirement specified.  
Downloading bundle ChimeraX_ISOLDE-1.5-cp39-cp39-macosx_10_13_universal2.whl  

> set bgColor black

> set bgColor white

Downloading bundle ChimeraX_ISOLDE-1.5-cp39-cp39-macosx_10_13_universal2.whl  
[Repeated 1 time(s)]




OpenGL version: 4.1 ATI-4.9.51
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 1916.80.2.0.0 (iBridge: 20.16.3045.0.0,0)
      OS Loader Version: 564.40.4~66

Software:

    System Software Overview:

      System Version: macOS 13.2 (22D49)
      Kernel Version: Darwin 22.3.0
      Time since boot: 18 days, 15 hours, 10 minutes

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-020
      Option ROM Version: 113-D32206U1-020
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        LG HDR WQHD:
          Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
          UI Looks like: 3440 x 1440 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 111NTJJ17772
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Adapter Type: DVI or HDMI
          Adapter Firmware Version: ff.c1


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    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: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 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: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    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-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    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-StarMap: 1.1.70
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    pyqtgraph: 0.13.1
    python-dateutil: 2.8.2
    pytz: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0
File attachment: SCR-20230214-n2k.png

SCR-20230214-n2k.png​

[ichcharisma@…]

Added by email2trac

[pett]

Reported by "Charisma"

[Tristan Croll]

For ChimeraX bundles (.whl files starting with "ChimeraX_") you need to use "toolshed install" rather than "pip install". Note that you need to download and install the ChimeraX_Clipper bundle before ISOLDE (you'll need to click on the "Release History" tab on Clipper's Toolshed page to get version 0.19.0, the last version compatible with ChimeraX 1.5). Could you see if that works for you?