Linux: No module named '_bz2'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1127.13.1.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open /home/binshtem/project/258-8-3/mr/Refine_26/cov3_2381_2.cxs format
> session

Log from Tue Jan 4 09:41:15 2022UCSF ChimeraX version: 1.3rc202111090815
(2021-11-09)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open /home/binshtem/project/258-8-3/mr/Refine_26/cov3_2381.cxs format
> session

Log from Sun Jan 2 18:39:32 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open D:\Refine_26\cov3_2381.cxs format session

Log from Sun Jan 2 17:47:05 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open D:\Refine_26\cov3_2381.cxs format session

Log from Sun Dec 19 20:38:14 2021UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open /media/elad/KINGSTON/Refine_26/cov3_2381.cxs format session

Log from Sat Dec 18 22:58:00 2021UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open /media/elad/KINGSTON/Refine_26/cov3_2381.cxs

Log from Fri Dec 17 17:16:43 2021 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/crowelab/Desktop/Refine_26/COV2-2381_refine_26.pdb

Chain information for COV2-2381_refine_26.pdb #1  
---  
Chain | Description  
A C F I | No description available  
B D G J | No description available  
E H K L | No description available  
  

> hide atoms

> show cartoons

> color bychain

> select E

Expected an objects specifier or a keyword  

> select /E

1550 atoms, 1599 bonds, 195 residues, 1 model selected  

> select /E,C,D

4815 atoms, 4944 bonds, 1 pseudobond, 625 residues, 2 models selected  

> show sel cartoons

> hide sel cartoons

> show sel cartoons

> select ~sel

14445 atoms, 14832 bonds, 3 pseudobonds, 1875 residues, 2 models selected  

> hide sel cartoons

> select ~sel

4815 atoms, 4944 bonds, 1 pseudobond, 625 residues, 2 models selected  

> view

> show sel surfaces

> select clear

> ui tool show Rotamers

No residues selected  

> hide surfaces

> show atoms

> hide atoms

> select /E,C,D

4815 atoms, 4944 bonds, 1 pseudobond, 625 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 4815 atom styles  

> style sel ball

Changed 4815 atom styles  

> select clear

> hbonds reveal true

2085 hydrogen bonds found  

> ~hbonds

> hide atoms

> select /E,C,D

4815 atoms, 4944 bonds, 1 pseudobond, 625 residues, 2 models selected  

> style sel ball

Changed 4815 atom styles  

> show sel atoms

> hbonds sel reveal true

521 hydrogen bonds found  

> select clear

> interfaces ~solvent

13 buried areas: J I 1710, D C 1706, G F 1694, B A 1689, I L 574, F H 525, C I
510, A K 502, C E 493, A F 484, K L 414, E H 399, D I 313  

> ~hbonds

> select clear

> hide atoms

> style stick

Changed 19260 atom styles  

> style sphere

Changed 19260 atom styles  

> style ball

Changed 19260 atom styles  

> style stick

Changed 19260 atom styles  

> hide cartoons

[Repeated 1 time(s)]

> hide atoms

[Repeated 1 time(s)]

> select /E,C,D

4815 atoms, 4944 bonds, 1 pseudobond, 625 residues, 2 models selected  

> show sel cartoons

> select clear

Drag select of 74 residues  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> hbonds sel reveal true

61 hydrogen bonds found  

> select clear

> ui tool show Rotamers

> select /E:478@CB

1 atom, 1 residue, 1 model selected  

> select /E:478@CB

1 atom, 1 residue, 1 model selected  

> select clear

> select /E:478@CB

1 atom, 1 residue, 1 model selected  

> ui tool show Rotamers

> select /E:478@CB

1 atom, 1 residue, 1 model selected  

> ui tool show Rotamers

> swapaa interactive sel ARG rotLib Dunbrack

/E THR 478: phi -72.2, psi 132.7 trans  
Changed 600 bond radii  

> select /E:481@CB

1 atom, 1 residue, 1 model selected  

> select /E:478@CB

1 atom, 1 residue, 1 model selected  

> select add /E:481@CB

2 atoms, 2 residues, 2 models selected  

> select subtract /E:481@CB

1 atom, 1 residue, 2 models selected  

> select add /E:481@CB

2 atoms, 2 residues, 2 models selected  

> distance /E:478@CB /E:481@CB

Distance between /E THR 478 CB and ASN 481 CB: 8.961Å  

> ui tool show Rotamers

> swapaa interactive sel ALA rotLib Dunbrack

> swapaa sel ALA rotLib Dunbrack

Using Dunbrack library  
Swapping /E THR 478 to ALA  
  
Swapping /E ASN 481 to ALA  
  
No residues selected  

> undo

[Repeated 3 time(s)]Undo failed, probably because structures have been
modified.  

> ui tool show Rotamers

> swapaa interactive sel THR rotLib Dunbrack

/E ALA 478: phi -72.2, psi 132.7 trans  
Changed 12 bond radii  

> swapaa #1/E:478 THR criteria 1 rotLib Dunbrack

Using Dunbrack library  
COV2-2381_refine_26.pdb #1/E ALA 478: phi -72.2, psi 132.7 trans  
Applying THR rotamer (chi angles: -59.6) to COV2-2381_refine_26.pdb #1/E THR
478  

> swapaa interactive sel ASN rotLib Dunbrack

/E ALA 481: phi 51.5, psi 28.4 trans  
Changed 180 bond radii  

> swapaa #1/E:481 ASN criteria 11 rotLib Dunbrack

Using Dunbrack library  
COV2-2381_refine_26.pdb #1/E ALA 481: phi 51.5, psi 28.4 trans  
Applying ASN rotamer (chi angles: -64.7 -93.2) to COV2-2381_refine_26.pdb #1/E
ASN 481  

> ui tool show Rotamers

> swapaa interactive sel THR rotLib Dunbrack

/E THR 478: phi -72.2, psi 132.7 trans  
Changed 12 bond radii  

> hbonds #!1 & ~#1/E:478 & ~solvent reveal true restrict #1.6 & ~@c,ca,n

1 hydrogen bonds found  

> swapaa interactive sel TYR rotLib Dunbrack

/E THR 478: phi -72.2, psi 132.7 trans  
Changed 180 bond radii  

> select clear

> select add /H:457@CD

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> show sel atoms

> hide sel atoms

> show sel atoms

Drag select of 12 atoms, 12 bonds  

> hide sel atoms

> select /H:465@OE2

1 atom, 1 residue, 1 model selected  

> select add /H:457@NH2

2 atoms, 2 residues, 1 model selected  

> hide sel atoms

Drag select of 4 atoms, 3 bonds  

> hide sel atoms

> select /E:481

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

> select clear

> select /E:481@OD1

1 atom, 1 residue, 1 model selected  

> select /E:481@OD1

1 atom, 1 residue, 1 model selected  

> select /E:481

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

> select clear

> interfaces ~solvent

13 buried areas: J I 1710, D C 1706, G F 1694, B A 1689, I L 574, F H 525, C I
510, A K 502, C E 492, A F 484, K L 414, E H 396, D I 313  

> select /E,C,D

4815 atoms, 4944 bonds, 1 pseudobond, 625 residues, 2 models selected  

> select clear

> hide sel atoms

> select clear

> select /E,C,D

4815 atoms, 4944 bonds, 1 pseudobond, 625 residues, 2 models selected  

> save /home/crowelab/Desktop/Refine_26/COV2-2381_refine_26_single.pdb
> selectedOnly true

> open /home/crowelab/Desktop/Refine_26/COV2-2381_refine_26_single.pdb

Summary of feedback from opening
/home/crowelab/Desktop/Refine_26/COV2-2381_refine_26_single.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 PHE A 29
SER A 31 1 3  
Start residue of secondary structure not found: HELIX 2 2 SER A 88 ASP A 90 1
3  
Start residue of secondary structure not found: HELIX 3 3 ASN A 165 GLY A 167
1 3  
Start residue of secondary structure not found: HELIX 4 4 SER A 196 LEU A 199
1 4  
Start residue of secondary structure not found: HELIX 5 5 LYS A 211 SER A 213
1 3  
170 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (22 )  
Cannot find LINK/SSBOND residue CYS (101 )  
Cannot find LINK/SSBOND residue CYS (150 )  
Cannot find LINK/SSBOND residue CYS (23 )  
Cannot find LINK/SSBOND residue CYS (136 )  
25 messages similar to the above omitted  
  
Chain information for COV2-2381_refine_26_single.pdb #4  
---  
Chain | Description  
C | No description available  
D | No description available  
E | No description available  
  

> hide #!1 models

> show #!1 models

> hide #!4 models

> select clear

> hide #3 models

> show #3 models

> hide #3 models

> hide #2 models

> close #2

> show #3 models

> close #3

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!1 models

> color #!4 bychain

[Repeated 1 time(s)]

> rainbow #!4

> color #!4 bypolymer

> color #!4 bychain

> interfaces #!4 & ~solvent

2 buried areas: D C 1706, C E 492  

> show sel atoms

> style sel sphere

Changed 185 atom styles  

> style sel ball

Changed 185 atom styles  

> show (sel-residues & sidechain) target ab

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

> label sel attribute label_one_letter_code

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

> label sel attribute label_specifier

> label sel text test

> label sel residues attribute number

> label sel residues attribute omega

> ui tool show "Selection Inspector"

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

> preset cartoons/nucleotides ribbons/slabs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

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

  

> preset cartoons/nucleotides cylinders/stubs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

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

  

> preset cartoons/nucleotides licorice/ovals

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

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

  

> show sel atoms

> preset "initial styles" "original look"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "initial styles" sticks

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "initial styles" cartoon

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "initial styles" "space-filling (chain colors)"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "initial styles" "space-filling (single color)"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "initial styles" "original look"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "molecular surfaces" "ghostly white"

Changed 19204 atom styles  
Preset expands to these ChimeraX commands:

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

  

> preset "molecular surfaces" "atomic coloring (transparent)"

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color fromatoms targ s trans 70

  

> preset "molecular surfaces" "chain id coloring (opaque)"

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

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

  

> hide sel surfaces

> show sel surfaces

> hide sel surfaces

> show sel surfaces

> preset "initial styles" "original look"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> preset "overall look" interactive

Preset expands to these ChimeraX commands:

    
    
    ~set bg
    graphics silhouettes f

  

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> show sel atoms

> color sel bychain

> select clear

> color #!4 bychain

> ui favorite true "Command Line Interface"

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

> select clear

> lighting flat

[Repeated 1 time(s)]

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting full

> lighting shadows false

> lighting shadows true

> lighting full

> lighting soft

> lighting flat

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting soft

> lighting full

> lighting soft

> lighting simple

> lighting full

> lighting simple

> lighting shadows true

> lighting shadows false

> lighting simple

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting soft

> lighting simple

> lighting soft

> lighting full

> lighting shadows false

> lighting soft

> show sel surfaces

> hide sel surfaces

> show sel surfaces

> select clear

> hide #!4 surfaces

> lighting soft

> lighting full

> lighting soft

> select clear

> ui tool show H-Bonds

> hbonds reveal true

3614 hydrogen bonds found  

> hbonds interModel false reveal true

2589 hydrogen bonds found  

> ~hbonds

> hbonds interModel false reveal true

2589 hydrogen bonds found  

> ~hbonds

> hbonds interModel false intraModel false intraRes false reveal true

0 hydrogen bonds found  

> hbonds interModel false intraModel false reveal true

0 hydrogen bonds found  

> hbonds interModel false reveal true

2589 hydrogen bonds found  

> ~hbonds

> hbonds intraModel false reveal true

1025 hydrogen bonds found  

> hbonds intraModel false reveal true

1025 hydrogen bonds found  

> hbonds reveal true

3614 hydrogen bonds found  

> ~hbonds

> hbonds sel restrict both reveal true

7 hydrogen bonds found  

> select clear

> open /home/crowelab/Desktop/Refine_26/COV2-2381_refine_26_2mFo-DFc.ccp4

Opened COV2-2381_refine_26_2mFo-DFc.ccp4 as #2, grid size 153,140,203, pixel
0.964,0.95,0.984, shown at level 3.2, step 1, values float32  

> volume #2 level 1.613

> surface dust #2 size 9.84

> color zone #2 near #4 distance 5.9

> hide #!2 models

Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.  

> volume show

> transparency #2.1#4.3,5 50

> volume style surface

[Repeated 1 time(s)]

> volume hide

Hide dust shortcut requires a displayed map surface  

Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.  

> volume show

> transparency #2#4.1-3,5-6#!4 0

> select #2

2 models selected  

> color zone #2 near #4 distance 5.9

> volume #2 level 0.4737

> volume #2 level 0.5

> volume #2 level 0.6

> select clear

> ui tool show "Surface Zone"

> surface zone #2 nearAtoms #4 distance 5.7

> view

> surface dust #2 size 9.84

[Repeated 1 time(s)]

> surface zone #2 nearAtoms #4 distance 4.5

> surface zone #2 nearAtoms #4 distance 4.4

> surface zone #2 nearAtoms #4 distance 4.3

> surface zone #2 nearAtoms #4 distance 4.2

> surface zone #2 nearAtoms #4 distance 4.1

> surface zone #2 nearAtoms #4 distance 4

> surface zone #2 nearAtoms #4 distance 3

> ui tool show "Hide Dust"

> surface dust #2 size 5.7

> surface undust #2

> surface dust #2 size 5.7

> surface dust #2 size 5.8

> surface dust #2 size 5.9

> surface dust #2 size 1

> surface dust #2 size 10

> surface zone #2 nearAtoms #4 distance 3

> transparency #2.1#4.3,5 50

> volume hide

> volume show

> hide #!2 models

> show #!2 models

> close #2

> select /E,C,D

9630 atoms, 9888 bonds, 9 pseudobonds, 1250 residues, 5 models selected  

> select clear

> select /C .3

Expected a keyword  

> select /C //3

Expected a keyword  

> select /C :3

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

> select clear

> ui tool show "Selection Inspector"

> save /home/crowelab/Desktop/Refine_26/cov3_2381.cxs

——— End of log from Fri Dec 17 17:16:43 2021 ———

opened ChimeraX session  

> hide #!4 atoms

> show #!4 atoms

> hide #!4 atoms

> ~hbonds

> ~label #4.1-3,5#!4 residues

> interfaces #!4 & ~solvent

2 buried areas: D C 1706, C E 492  
Matplotlib is building the font cache; this may take a moment.  

> style sel ball

Changed 185 atom styles  

> show sel atoms

> hbonds sel reveal true

63 hydrogen bonds found  

> ~hbonds

> ui tool show Contacts

> ui tool show "Color Actions"

> ui tool show Contacts

> label (#!4 & sel) attribute name

> label (#!4 & sel) attribute label_specifier

> label (#!4 & sel) text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

> contacts sel restrict both select true

64 contacts  

> contacts sel restrict both intraMol false select true

28 contacts  

> color list

No custom colors.  
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

.  

> label (#!4 & sel) text "/ {0.name} {0.number}{0.insertion_code}"

> save /media/elad/KINGSTON/Refine_26/cov3_2381.cxs

> ui tool show "Basic Actions"

> ui tool show "Color Key"

> ui mousemode right "color key"

> key blue-white-red :min : :max white:

> key blue-white-red :min : :max

> key delete

> ui mousemode right translate

> ui tool show H-Bonds

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> select clear

> interfaces #!4 & ~solvent

2 buried areas: D C 1706, C E 492  

> hbonds saltOnly true

210 hydrogen bonds found  

> hbonds sel restrict both saltOnly true

0 hydrogen bonds found  

> hbonds sel restrict both

7 hydrogen bonds found  

> hbonds sel color #f57900 restrict both

7 hydrogen bonds found  

> hbonds sel color #edd400 restrict both

7 hydrogen bonds found  

> hbonds sel color #edd400 restrict both intraRes false

7 hydrogen bonds found  

> hbonds sel color #edd400 restrict both intraMol false intraRes false

4 hydrogen bonds found  

> hbonds sel color #edd400 restrict both intraRes false

7 hydrogen bonds found  

> hbonds sel color #edd400 restrict both intraMol false intraRes false

4 hydrogen bonds found  

> hbonds sel color #edd400 radius 0.095 restrict both intraMol false intraRes
> false

4 hydrogen bonds found  

> label (#!4 & sel) text "/ {0.name} {0.number}{0.insertion_code}"

Height must be a number  

> label height 1

Height must be a number  

> label height 2

> label height 1

> save /media/elad/KINGSTON/Refine_26/cov3_2381.cxs

> view

> view sel

> view

> view sel

> ui tool show "Side View"

> view sel

[Repeated 2 time(s)]

> view orient

> view sel

[Repeated 2 time(s)]

> label (#!4 & sel) text "{0.name} {0.number}{0.insertion_code}"

> select clear

> preset cartoons/nucleotides licorice/ovals

Changed 19204 atom styles  
Preset expands to these ChimeraX commands:

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

  

> undo

> show #!1 models

> hide #!1 models

> select #4/C:75

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

> select clear

> ui mousemode right label

> label #4/C:66

> label #4/E:405

> ui mousemode right "move label"

> label (#!4 & sel) text "{0.name} {0.number}"

> select #4/E:406

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

> label (#!4 & sel) text "{0.name} {0.number}"

> label (#!4 & sel) text "{0.name} {0.number}{0.insertion_code}"

> select #4/E:405

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

> label (#!4 & sel) text "{0.name} {0.number}{0.insertion_code}"

> ui mousemode right label

> ui mousemode right select

> color sel bychain

> select #4/E:405

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

> ui mousemode right label

> label #4/E:405

> color sel bychain

> label (#!4 & sel) text "{0.name} {0.number}{0.insertion_code}" color bychian

Invalid "color" argument: Expected one of 'auto' or 'default' or a color  

> label (#!4 & sel) text "{0.name} {0.number}{0.insertion_code}" color bychain

Invalid "color" argument: Expected one of 'auto' or 'default' or a color  

> label (#!4 & sel) text "{0.name} {0.number}{0.insertion_code}" color auto

> color bychain labels

> label #4/E:406

> color red labels

> color bychain labels

> color auto l

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

> label (#!4 & sel) text "{0.name} {0.number}{0.insertion_code}" color auto

> color bychain labels

> color red labels

> undo

[Repeated 9 time(s)]

> ui mousemode right label

> ui mousemode right translate

> select clear

> view sel

[Repeated 1 time(s)]

> save /media/elad/KINGSTON/Refine_26/cov3_2381.cxs

——— End of log from Sat Dec 18 22:58:00 2021 ———

opened ChimeraX session  

> select /E : 339,373,375,440,446,496,498,501,505

122 atoms, 106 bonds, 18 residues, 2 models selected  

> color (#!4 & sel) yellow

> color (#!4 & sel) orange

> select /E : 417,477,478,484,493

80 atoms, 72 bonds, 10 residues, 2 models selected  

> color (#!4 & sel) red

> select clear

> save /media/elad/KINGSTON/Refine_26/cov3_2381.cxs

——— End of log from Sun Dec 19 20:38:14 2021 ———

opened ChimeraX session  

> select #4 /E :371

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

> color (#!4 & sel) orange

> open 7t9k

Summary of feedback from opening 7t9k fetched from pdb  
---  
notes | Fetching compressed mmCIF 7t9k from
http://files.rcsb.org/download/7t9k.cif  
Fetching CCD NAG from http://ligand-expo.rcsb.org/reports/N/NAG/NAG.cif  
  
7t9k title:  
Cryo-EM structure of SARS-CoV-2 ο spike protein in complex with human ACE2
[more info...]  
  
Chain information for 7t9k #3  
---  
Chain | Description | UniProt  
A B C | Spike glycoprotein | SPIKE_SARS2  
D E | Processed angiotensin-converting enzyme 2 | ACE2_HUMAN  
  
Non-standard residues in 7t9k #3  
---  
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)  
  

> save D:/Refine_26/cov3_2381.cxs

> hide #!3 models

> hide #2 models

> hide #!4 models

> show #!3 models

> select #4

4815 atoms, 4944 bonds, 65 pseudobonds, 625 residues, 6 models selected  

> ~select #4

3 models selected  

> select #3 /A

8213 atoms, 8425 bonds, 8 pseudobonds, 1040 residues, 2 models selected  

> save D:/Refine_26/7T9K_omicron_single.pdb models #3 selectedOnly true

> close #3

> open D:/Refine_26/7T9K_omicron_single.pdb

Summary of feedback from opening D:/Refine_26/7T9K_omicron_single.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 21 21 ASP B
294 LYS B 304 1 11  
Start residue of secondary structure not found: HELIX 22 22 PRO B 337 ASN B
343 1 7  
Start residue of secondary structure not found: HELIX 23 23 TYR B 365 ASN B
370 1 6  
Start residue of secondary structure not found: HELIX 24 24 PRO B 384 ASN B
388 1 5  
Start residue of secondary structure not found: HELIX 25 25 GLY B 416 ASN B
422 1 7  
204 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (15 )  
Cannot find LINK/SSBOND residue CYS (131 )  
Cannot find LINK/SSBOND residue CYS (291 )  
Cannot find LINK/SSBOND residue CYS (336 )  
Cannot find LINK/SSBOND residue CYS (379 )  
84 messages similar to the above omitted  
  
Chain information for 7T9K_omicron_single.pdb #3  
---  
Chain | Description  
A | No description available  
  

> show #!4 models

> ui tool show Matchmaker

> matchmaker #!3 to #4

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 COV2-2381_refine_26_single.pdb, chain E (#4) with
7T9K_omicron_single.pdb, chain A (#3), sequence alignment score = 861  
RMSD between 186 pruned atom pairs is 0.733 angstroms; (across all 194 pairs:
0.899)  
  

> save D:/Refine_26/cov3_2381.cxs

——— End of log from Sun Jan 2 17:47:05 2022 ———

opened ChimeraX session  

> close #3

> open D:/Refine_26/7T9K_omicron_single.pdb

Chain information for 7T9K_omicron_single.pdb #3  
---  
Chain | Description  
A | No description available  
  

> ui tool show Matchmaker

> matchmaker #!3 to #4

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 COV2-2381_refine_26_single.pdb, chain E (#4) with
7T9K_omicron_single.pdb, chain A (#3), sequence alignment score = 861  
RMSD between 186 pruned atom pairs is 0.733 angstroms; (across all 194 pairs:
0.899)  
  

> hide #!4 models

> cartoon style #3 xsection oval width 1 thickness 1

> show #!4 models

> save D:/Refine_26/cov3_2381.cxs

> select #3 /A :417, 493, 477, 478

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

> hide #!3 models

> style #4.1-3,5-7#!4 ball

Changed 4815 atom styles  

> show (#4.1-3,5-7#!4 & sidechain) target ab

> undo

> show #!3 models

> show (sel-residues & sidechain) target ab

> style sel ball

Changed 36 atom styles  

> select #3

8213 atoms, 8425 bonds, 8 pseudobonds, 1040 residues, 2 models selected  

> hide sel cartoons

> select clear

> save D:/Refine_26/cov3_2381.cxs

——— End of log from Sun Jan 2 18:39:32 2022 ———

opened ChimeraX session  

> ui tool show H-Bonds

> show #2 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #2 models

> show #2 models

> hide #!1 models

> hide #2 models

> select add #4/E:477

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

> select add #4/E:478

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

> select add #4/E:484

22 atoms, 19 bonds, 3 residues, 2 models selected  

> select add #4/E:493

31 atoms, 27 bonds, 4 residues, 2 models selected  

> select add #4/E:417@CG

32 atoms, 27 bonds, 5 residues, 2 models selected  

> select up

40 atoms, 36 bonds, 5 residues, 2 models selected  

> select up

362 atoms, 371 bonds, 45 residues, 2 models selected  

> select down

40 atoms, 36 bonds, 5 residues, 2 models selected  

> select add #4/E:475

45 atoms, 40 bonds, 6 residues, 2 models selected  

> hbonds sel color #fce94f interModel false distSlop 0.5 intraMol false reveal
> true

5 hydrogen bonds found  

> hbonds sel color #fce94f interModel false distSlop 0.5 intraMol false reveal
> true

5 hydrogen bonds found  

> hbonds sel color #8ae234 interModel false distSlop 0.5 intraMol false reveal
> true

5 hydrogen bonds found  

> hbonds sel color #fce94f radius 0.1 interModel false distSlop 0.5 intraMol
> false reveal true

5 hydrogen bonds found  

> select #4/C:57

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

> hbonds sel color #fce94f radius 0.1 interModel false distSlop 0.5 intraMol
> false reveal true

0 hydrogen bonds found  

> show (#!4 & sel-residues & sidechain) target ab

> select #4/E:493

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

> select add #4/E:477

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

> select add #4/E:478

22 atoms, 19 bonds, 3 residues, 2 models selected  

> select add #4/E:475

27 atoms, 23 bonds, 4 residues, 2 models selected  

> select add #4/E:487

35 atoms, 30 bonds, 5 residues, 2 models selected  

> hbonds sel color #fce94f radius 0.1 interModel false distSlop 0.5 intraMol
> false reveal true

6 hydrogen bonds found  

> ui mousemode right distance

> distance #4/E:493@NE2 #4/C:57@OD1

Distance between COV2-2381_refine_26_single.pdb #4/E GLN 493 NE2 and /C ASN 57
OD1: 3.072Å  

> hide #5.1 models

> save /home/binshtem/project/258-8-3/mr/Refine_26/cov3_2381_2.cxs

——— End of log from Tue Jan 4 09:41:15 2022 ———

opened ChimeraX session  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> select clear

> interfaces #!3-4 & ~solvent

4 buried areas: #3/A #4/E 5090, #4/D #4/C 1706, #3/A #4/C 537, #4/C #4/E 492  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/toolbar/tool.py", line 205, in
callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/toolshed/info.py", line
381, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/toolshed/__init__.py", line
1284, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/shortcuts/__init__.py", line 52,
in run_provider  
shortcuts.run_provider(session, name)  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py", line
1334, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py", line
390, in try_shortcut  
self.run_shortcut(keys)  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py", line
408, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py", line
327, in run  
f(s)  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py", line
569, in run_expanded_command  
run(session, cmd)  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py", line
512, in run  
run_command(session, command, **kw)  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 36,
in run  
results = command.run(text, log=log, return_json=return_json)  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line
2856, in run  
result = ci.function(session, **kw_args)  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/interfaces/cmd.py", line 49, in
interfaces  
tool.ContactPlot(session, sg, ba, interface_residue_area_cutoff)  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/interfaces/tool.py", line 25, in
__init__  
Graph.__init__(self, session, groups, contacts,  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/interfaces/graph.py", line 139,
in __init__  
self.graph = self._make_graph()  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/interfaces/graph.py", line 160,
in _make_graph  
import networkx as nx  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/networkx/__init__.py", line 57, in
<module>  
from networkx import utils  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/networkx/utils/__init__.py", line 2, in
<module>  
from networkx.utils.decorators import *  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/networkx/utils/decorators.py", line 12,
in <module>  
import re, gzip, bz2  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/bz2.py", line 18, in <module>  
from _bz2 import BZ2Compressor, BZ2Decompressor  
ModuleNotFoundError: No module named '_bz2'  
  
ModuleNotFoundError: No module named '_bz2'  
  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/bz2.py", line 18, in  
from _bz2 import BZ2Compressor, BZ2Decompressor  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 460.84
OpenGL renderer: GeForce RTX 2080 SUPER/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Micro-Star International Co., Ltd.
Model: MS-7A94
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 36 Intel(R) Core(TM) i9-9980XE CPU @ 3.00GHz
Cache Size: 25344 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           125G         14G         98G        484M         12G        110G
	Swap:          5.6G          0B        5.6G

Graphics:
	65:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU104 [GeForce RTX 2080 SUPER] [10de:1e81] (rev a1)	
	Subsystem: Micro-Star International Co., Ltd. [MSI] Device [1462:c724]	
	Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.3
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    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
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

[Greg Couch]

Added bzip2 development libraries to the CentOS 7 and CentOS 8 images used to build ChimeraX.