The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Volumes/GoogleDrive/My Drive/PLESS_LAB/Labpics/ASIC1-PcTx1.cxs"
Log from Fri Apr 22 15:36:01 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Volumes/GoogleDrive/My Drive/PLESS_LAB/PcTx_manuscript/Fig1.cxs"
> format session
Log from Fri Apr 23 19:53:48 2021UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open P:\PcTx_manuscript\Fig1.cxs format session
Log from Thu Apr 22 23:58:19 2021UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open C:\Users\zck761\AppData\Local\Temp\4fz0.cif format mmcif
4fz0.cif title:
Crystal structure of acid-sensing ion channel in complex with psalmotoxin 1 at
low pH [more info...]
Chain information for 4fz0.cif #1
---
Chain | Description
A B C | Acid-sensing ion channel 1
M N O | Pi-theraphotoxin-Pc1a
Non-standard residues in 4fz0.cif #1
---
CL — chloride ion
GOL — glycerol (glycerin; propane-1,2,3-triol)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> ui tool show "Side View"
> ui mousemode right "rotate selected models"
> ui mousemode right "mark point"
> set bgColor white
> lighting soft
> lighting flat
> lighting soft
> graphics silhouettes false
> view orient
> view orient
> view orient
> view orient
> ui tool show "Side View"
> view
> view
> lighting simple
> lighting simple
> lighting simple
> lighting full
> lighting soft
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes true
> graphics silhouettes false
> transparency 50
> volume style surface
No volumes specified
> volume projectionMode 2d-xyz
No volumes specified
> volume projectionMode 3d
No volumes specified
> volume appearance initial
No volumes specified
> ui mousemode right "mark point"
> ui mousemode right "mark center"
> ui mousemode right "mark surface"
> ui mousemode right "mark plane"
> ui mousemode right "mark maximum"
> ui mousemode right "translate selected models"
> ui mousemode right "contour level"
> ui mousemode right "contour level"
> ui mousemode right "pick blobs"
> help help:index.html
> help help:quickstart
> volume showOutlineBox true
No volumes specified
> set bgColor black
> set bgColor white
> lighting soft
> lighting full
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting soft
> view clip false
> view clip false
> view
> nucleotides tube/slab shape box
> nucleotides tube/slab shape muffler
> toolshed show
> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html
Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html
> open 2bbv
Summary of feedback from opening 2bbv fetched from pdb
---
notes | Fetching compressed mmCIF 2bbv from
http://files.rcsb.org/download/2bbv.cif
Fetching CCD CA from http://ligand-expo.rcsb.org/reports/C/CA/CA.cif
2bbv title:
The refined three-dimensional structure of an insect virus At 2.8 angstroms
resolution [more info...]
Chain information for 2bbv #2
---
Chain | Description
A B C | protein (black beetle virus capsid protein)
D E F | protein (black beetle virus capsid protein)
N | RNA (5'-R(*up*CP*up*up*ap*up*ap*up*CP*U)-3')
Non-standard residues in 2bbv #2
---
CA — calcium ion
2bbv mmCIF Assemblies
---
1| complete icosahedral assembly
2| icosahedral asymmetric unit
3| icosahedral pentamer
4| icosahedral 23 hexamer
5| icosahedral asymmetric unit, std point frame
6| crystal asymmetric unit, crystal frame
> lighting full
> close session
> open 2bbv format mmcif fromDatabase pdb
2bbv title:
The refined three-dimensional structure of an insect virus At 2.8 angstroms
resolution [more info...]
Chain information for 2bbv #1
---
Chain | Description
A B C | protein (black beetle virus capsid protein)
D E F | protein (black beetle virus capsid protein)
N | RNA (5'-R(*up*CP*up*up*ap*up*ap*up*CP*U)-3')
Non-standard residues in 2bbv #1
---
CA — calcium ion
2bbv mmCIF Assemblies
---
1| complete icosahedral assembly
2| icosahedral asymmetric unit
3| icosahedral pentamer
4| icosahedral 23 hexamer
5| icosahedral asymmetric unit, std point frame
6| crystal asymmetric unit, crystal frame
> style /b stick
Changed 2382 atom styles
> hide /c
> hide /c
> close session
> open C:\Users\zck761\AppData\Local\Temp\4fz0.cif format mmcif
4fz0.cif title:
Crystal structure of acid-sensing ion channel in complex with psalmotoxin 1 at
low pH [more info...]
Chain information for 4fz0.cif #1
---
Chain | Description
A B C | Acid-sensing ion channel 1
M N O | Pi-theraphotoxin-Pc1a
Non-standard residues in 4fz0.cif #1
---
CL — chloride ion
GOL — glycerol (glycerin; propane-1,2,3-triol)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose
> select :.A
Expected an objects specifier or a keyword
> select :.A
Expected an objects specifier or a keyword
> select :A
Nothing selected
> select .:A
Expected an objects specifier or a keyword
> select .A
Expected an objects specifier or a keyword
> select :.A
Expected an objects specifier or a keyword
> select :106
28 atoms, 24 bonds, 4 residues, 1 model selected
> select :.
Expected an objects specifier or a keyword
> select all
10557 atoms, 10686 bonds, 1486 residues, 1 model selected
> hide sel atoms
> show sel atoms
> show sel cartoons
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> preset cartoons/nucleotides cylinders/stubs
Changed 10328 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 "molecular surfaces" "ghostly white"
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> preset 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
> hide (#!1 & sel) target a
> select clear
> select /B:60
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
140 atoms, 142 bonds, 22 residues, 2 models selected
> select up
3199 atoms, 3234 bonds, 454 residues, 2 models selected
> color (#!1 & sel) dark gray
> select clear
> select up
163 atoms, 171 bonds, 22 residues, 2 models selected
> select up
3184 atoms, 3227 bonds, 445 residues, 2 models selected
> color (#!1 & sel) dark gray
> ui tool show "Color Actions"
> color sel light slate gray
> color sel slate gray
> color sel silver
> color sel tan
> color sel silver
> select clear
> select up
92 atoms, 91 bonds, 12 residues, 2 models selected
> select up
3199 atoms, 3234 bonds, 454 residues, 2 models selected
> color sel dim gray
> color sel dark gray
> color sel light slate gray
> select clear
> select up
189 atoms, 192 bonds, 27 residues, 2 models selected
> select up
3282 atoms, 3314 bonds, 463 residues, 2 models selected
> color sel white
> select clear
> select up
140 atoms, 142 bonds, 22 residues, 2 models selected
> select up
3199 atoms, 3234 bonds, 454 residues, 2 models selected
> select up
3298 atoms, 3332 bonds, 466 residues, 3 models selected
> select up
6383 atoms, 6461 bonds, 899 residues, 3 models selected
> show sel atoms
> style sel sphere
Changed 6383 atom styles
> lighting soft
> select clear
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
35 atoms, 37 bonds, 4 residues, 2 models selected
> select up
3199 atoms, 3234 bonds, 454 residues, 2 models selected
> color sel white
> lighting full
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> show sel surfaces
> cartoon style (#!1 & sel) modeHelix tube sides 20
> hide sel surfaces
> hide sel cartoons
> select clear
> select up
175 atoms, 180 bonds, 23 residues, 3 models selected
> select up
585 atoms, 598 bonds, 81 residues, 3 models selected
> color (#!1 & sel) #fdfffeff
> color (#!1 & sel) #eaffedff
> color (#!1 & sel) #2dff42ff
> color (#!1 & sel) #eaffedff
> color (#!1 & sel) #fdfffeff
> color (#!1 & sel) #ebffedff
> color (#!1 & sel) #36ff4aff
> color (#!1 & sel) #010702ff
> color (#!1 & sel) #104c16ff
> color (#!1 & sel) #100116ff
> color (#!1 & sel) #100d16ff
> color (#!1 & sel) #108816ff
> color (#!1 & sel) #108801ff
> color (#!1 & sel) #10880dff
> color (#!1 & sel) #108885ff
> color (#!1 & sel) #d2e7f8ff
> color (#!1 & sel) #ffffffff
> color (#!1 & sel) #f0f0f0ff
> color (#!1 & sel) #000000ff
> color (#!1 & sel) #ffffffff
QWindowsWindow::setGeometry: Unable to set geometry 2x2+212+664 (frame:
2x2+212+664) on QWindow/"" on "\\\\.\DISPLAY2". Resulting geometry:
3x3+212+664 (frame: 3x3+212+664) margins: 0, 0, 0, 0)
> color (#!1 & sel) #000000ff
> color (#!1 & sel) #ffffffff
> color (#!1 & sel) #483d8bff
> color (#!1 & sel) #000000ff
> color (#!1 & sel) #e1e1e1ff
> color (#!1 & sel) #f0f0f0ff
> color (#!1 & sel) #b1c8aaff
> color (#!1 & sel) #f0f0f0ff
> color (#!1 & sel) #ffffffff
> color (#!1 & sel) #108885ff
> select clear
> select up
37 atoms, 38 bonds, 4 residues, 2 models selected
> select up
307 atoms, 313 bonds, 43 residues, 2 models selected
> select clear
> select up
37 atoms, 38 bonds, 4 residues, 2 models selected
> select up
307 atoms, 313 bonds, 43 residues, 2 models selected
> color sel blue
> color (#!1 & sel) #d7eaf8ff
> color (#!1 & sel) #ccccccff
> color (#!1 & sel) #ccccb1ff
> color (#!1 & sel) #108885ff
> select clear
> select up
157 atoms, 157 bonds, 24 residues, 2 models selected
> select up
3282 atoms, 3314 bonds, 463 residues, 2 models selected
> color sel slate gray
> color sel dark gray
> color sel dim gray
> select clear
> select up
4 atoms, 3 bonds, 1 residue, 2 models selected
> select up
115 atoms, 118 bonds, 15 residues, 2 models selected
> select up
3199 atoms, 3234 bonds, 454 residues, 2 models selected
> show sel surfaces
> select clear
> lighting full
> lighting simple
> lighting soft
> view
> transparency 30
> lighting soft
> lighting soft
> lighting full
> lighting soft
> select up
157 atoms, 157 bonds, 24 residues, 2 models selected
> select up
3282 atoms, 3314 bonds, 463 residues, 2 models selected
> color (#!1 & sel) white
> select clear
> graphics silhouettes true
> select :.106
Expected an objects specifier or a keyword
> select :106
28 atoms, 24 bonds, 4 residues, 1 model selected
> show (#!1 & sel) target ab
> ui tool show "Color Actions"
> color sel crimson
> color sel tomato
> color sel tomato
> select :81
21 atoms, 18 bonds, 3 residues, 1 model selected
> show (#!1 & sel) target ab
> ui tool show "Color Actions"
> color sel tomato
> color sel tomato
> select clear
> select up
12 atoms, 12 bonds, 1 residue, 2 models selected
> select up
140 atoms, 142 bonds, 22 residues, 2 models selected
> select up
3199 atoms, 3234 bonds, 454 residues, 2 models selected
> hide sel surfaces
> preset cartoons/nucleotides cylinders/stubs
Changed 6339 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
> select clear
> select up
313 atoms, 322 bonds, 42 residues, 4 models selected
> select up
892 atoms, 911 bonds, 124 residues, 4 models selected
> show sel surfaces
> select :81
21 atoms, 18 bonds, 3 residues, 1 model selected
> show sel atoms
> show (#!1 & sel-residues & sidechain) target ab
> nucleotides sel fill
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel tube/slab shape box
> nucleotides sel fill
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel sphere
Changed 21 atom styles
> select up
384 atoms, 387 bonds, 51 residues, 4 models selected
> select up
9665 atoms, 9775 bonds, 1362 residues, 4 models selected
> select up
10557 atoms, 10686 bonds, 1486 residues, 4 models selected
> hide (#!1 & sel) target a
> select :81
21 atoms, 18 bonds, 3 residues, 1 model selected
> show (#!1 & sel) target ab
> select :106
28 atoms, 24 bonds, 4 residues, 1 model selected
> show (#!1 & sel) target ab
> style sel sphere
Changed 28 atom styles
> select clear
> select up
92 atoms, 91 bonds, 12 residues, 2 models selected
> select up
3199 atoms, 3234 bonds, 454 residues, 2 models selected
> select up
3298 atoms, 3332 bonds, 466 residues, 3 models selected
> select up
6383 atoms, 6461 bonds, 899 residues, 3 models selected
> show sel surfaces
> select clear
> select up
157 atoms, 157 bonds, 24 residues, 2 models selected
> select up
3282 atoms, 3314 bonds, 463 residues, 2 models selected
> color sel dark gray
> color sel dim gray
> select clear
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting flat
> lighting soft
> ui tool show "Side View"
> select :106
28 atoms, 24 bonds, 4 residues, 1 model selected
> ui tool show "Color Actions"
> color sel tomato
> color sel tomato
> select :81
21 atoms, 18 bonds, 3 residues, 1 model selected
> ui tool show "Color Actions"
> color sel tomato
> select clear
> select up
7 atoms, 7 bonds, 1 residue, 2 models selected
> select up
35 atoms, 37 bonds, 4 residues, 2 models selected
> select up
3199 atoms, 3234 bonds, 454 residues, 2 models selected
> select up
3204 atoms, 3238 bonds, 455 residues, 3 models selected
> select up
3362 atoms, 3405 bonds, 476 residues, 3 models selected
> select up
6383 atoms, 6461 bonds, 899 residues, 3 models selected
> transparency (#!1 & sel) 0
> select clear
> lighting soft
> style sphere
Changed 10557 atom styles
> hide surfaces
> select up
140 atoms, 142 bonds, 22 residues, 2 models selected
> select up
3199 atoms, 3234 bonds, 454 residues, 2 models selected
> select up
3298 atoms, 3332 bonds, 466 residues, 3 models selected
> select up
6383 atoms, 6461 bonds, 899 residues, 3 models selected
> show sel atoms
> hide sel atoms
> show sel surfaces
> select clear
> select up
150 atoms, 150 bonds, 19 residues, 2 models selected
> select up
3282 atoms, 3314 bonds, 463 residues, 2 models selected
> color (#!1 & sel) white
> select clear
> select up
14 atoms, 15 bonds, 1 residue, 2 models selected
> select up
163 atoms, 171 bonds, 22 residues, 2 models selected
> select up
3199 atoms, 3234 bonds, 454 residues, 2 models selected
> color (#!1 & sel) dark gray
> select clear
> select /A:367@ND2
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
105 atoms, 105 bonds, 13 residues, 2 models selected
> select up
3184 atoms, 3227 bonds, 445 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light salmon
> color sel mint cream
> color sel honeydew
> select clear
> select up
11 atoms, 11 bonds, 1 residue, 2 models selected
> select up
35 atoms, 37 bonds, 4 residues, 2 models selected
> select up
3199 atoms, 3234 bonds, 454 residues, 2 models selected
> color sel beige
> color sel alice blue
> color sel light cyan
> color sel antique white
> color sel linen
> select clear
> select /B:71@CB
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 2 models selected
> select up
35 atoms, 37 bonds, 4 residues, 2 models selected
> select up
3199 atoms, 3234 bonds, 454 residues, 2 models selected
> color sel old lace
> color sel light goldenrod yellow
> select clear
> select up
101 atoms, 103 bonds, 12 residues, 4 models selected
> select up
892 atoms, 911 bonds, 124 residues, 4 models selected
> show sel surfaces
> select clear
> select :81
21 atoms, 18 bonds, 3 residues, 1 model selected
> color sel tomato
> select :106
28 atoms, 24 bonds, 4 residues, 1 model selected
> color sel tomato
> select /A:285@CG
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 2 residues, 3 models selected
> select up
320 atoms, 328 bonds, 46 residues, 3 models selected
> select up
6466 atoms, 6541 bonds, 908 residues, 3 models selected
> select down
320 atoms, 328 bonds, 46 residues, 3 models selected
> select clear
> select /B:67@CB
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 2 models selected
> select up
140 atoms, 142 bonds, 22 residues, 2 models selected
> select up
3199 atoms, 3234 bonds, 454 residues, 2 models selected
> color sel light cyan
> select clear
> select up
5 atoms, 4 bonds, 1 residue, 2 models selected
> select up
140 atoms, 142 bonds, 22 residues, 2 models selected
> select up
3199 atoms, 3234 bonds, 454 residues, 2 models selected
> color sel beige
> color sel azure
> select clear
> select clear
> select /C:440
8 atoms, 7 bonds, 1 residue, 1 model selected
> lighting full
> lighting simple
> lighting flat
> lighting shadows true intensity 0.5
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> graphics silhouettes false
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> select clear
> select /A:426@OE2
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
31 atoms, 31 bonds, 4 residues, 2 models selected
> select up
3184 atoms, 3227 bonds, 445 residues, 2 models selected
> hide sel surfaces
> select clear
> show atoms
> undo
> select up
99 atoms, 98 bonds, 12 residues, 2 models selected
> select up
3184 atoms, 3227 bonds, 445 residues, 2 models selected
> show sel surfaces
> select clear
> select up
189 atoms, 192 bonds, 27 residues, 2 models selected
> select up
3282 atoms, 3314 bonds, 463 residues, 2 models selected
> color sel dim gray
> color sel black
> color sel dim gray
> select clear
> undo
> undo
> undo
> undo
> undo
> select clear
> select up
5 atoms, 4 bonds, 1 residue, 2 models selected
> select up
35 atoms, 37 bonds, 4 residues, 2 models selected
> select up
3199 atoms, 3234 bonds, 454 residues, 2 models selected
> color sel slate gray
> select clear
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
105 atoms, 105 bonds, 13 residues, 2 models selected
> select up
3184 atoms, 3227 bonds, 445 residues, 2 models selected
> color sel dark olive green
> select clear
> select up
189 atoms, 192 bonds, 27 residues, 2 models selected
> select up
3282 atoms, 3314 bonds, 463 residues, 2 models selected
> show sel surfaces
> select clear
> undo
> undo
> undo
> hide sel surfaces
> select up
3294 atoms, 3326 bonds, 464 residues, 3 models selected
> select up
3422 atoms, 3456 bonds, 485 residues, 3 models selected
> select up
6481 atoms, 6548 bonds, 917 residues, 3 models selected
> select up
6495 atoms, 6563 bonds, 918 residues, 4 models selected
> select up
6644 atoms, 6719 bonds, 939 residues, 4 models selected
> select up
9665 atoms, 9775 bonds, 1362 residues, 4 models selected
> hide sel surfaces
> select clear
> select up
157 atoms, 159 bonds, 24 residues, 3 models selected
> select up
6481 atoms, 6548 bonds, 917 residues, 3 models selected
> color sel white smoke
> color sel powder blue
> select clear
> select up
140 atoms, 142 bonds, 22 residues, 2 models selected
> select up
3199 atoms, 3234 bonds, 454 residues, 2 models selected
> color sel old lace
> color sel linen
> color sel honeydew
> select clear
> select up
46 atoms, 46 bonds, 5 residues, 2 models selected
> select up
3184 atoms, 3227 bonds, 445 residues, 2 models selected
> color sel light blue
> graphics silhouettes false
> lighting full
> lighting full
> lighting soft
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> style radius 3.0
Expected a keyword
> style radius 2.0
Expected a keyword
> cartoon style radius 2.0
> cartoon style radius 2.0
> cartoon style radius 4.0
> cartoon style radius 2.5
> cartoon style radius 2.0
> cartoon style radius 2.5
> cartoon style radius default
Invalid "radius" argument: Expected a number or 'auto'
> cartoon style radius auto
> select up
3324 atoms, 3369 bonds, 467 residues, 3 models selected
> select up
6383 atoms, 6461 bonds, 899 residues, 3 models selected
> select up
10557 atoms, 10686 bonds, 1486 residues, 3 models selected
> cartoon style radius auto
> cartoon style radius 2.3
> cartoon style radius 2.0
> cartoon style arrows false
> cartoon style widh 2.5
Expected an atoms specifier or a keyword
> cartoon style width 2.5
> cartoon style width 2.0
> cartoon style width 2.5
> cartoon style width 2.0
> cartoon style thickness 0.3
> cartoon style thickness 0.6
> cartoon style thickness 0.8
> cartoon style thickness 1
> cartoon style heliz 2.5
Expected an atoms specifier or a keyword
> cartoon style helix 2.5
Expected a keyword
> cartoon style helix 2.5
Expected a keyword
> cartoon style radius 2.5
> select clear
> select up
157 atoms, 157 bonds, 24 residues, 2 models selected
> select up
3282 atoms, 3314 bonds, 463 residues, 2 models selected
> color (#!1 & sel) white
> select clear
> select up
282 atoms, 284 bonds, 48 residues, 3 models selected
> select up
6383 atoms, 6461 bonds, 899 residues, 3 models selected
> show sel surfaces
> select clear
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
163 atoms, 171 bonds, 22 residues, 2 models selected
> select up
3184 atoms, 3227 bonds, 445 residues, 2 models selected
> ui tool show "Color Actions"
> color sel honeydew
> select clear
> select up
189 atoms, 192 bonds, 27 residues, 2 models selected
> select up
3282 atoms, 3314 bonds, 463 residues, 2 models selected
> color sel light gray
> select clear
> select /C:57
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
189 atoms, 192 bonds, 27 residues, 2 models selected
> select up
3282 atoms, 3314 bonds, 463 residues, 2 models selected
> color sel rosy brown
> color sel light slate gray
> color sel blue
> color sel deep sky blue
> color sel light blue
> color sel silver
> color sel wheat
> color sel rosy brown
> color sel tan
> color sel moccasin
> color sel navajo white
> color sel peach puff
> color sel black
> color sel burly wood
> color sel rosy brown
> color (#!1 & sel) #aaaa7fff
> color (#!1 & sel) #a8aa7fff
> color (#!1 & sel) #aaa272ff
> color (#!1 & sel) #aaa06eff
> color (#!1 & sel) #aa9f63ff
> color (#!1 & sel) #aa9f62ff
> color (#!1 & sel) #aa9c4aff
> color (#!1 & sel) #aa9a4aff
> color (#!1 & sel) #aa8046ff
> color (#!1 & sel) #aa7b44ff
> color (#!1 & sel) #aa7744ff
> color (#!1 & sel) #ad7946ff
> color (#!1 & sel) #c1884eff
> color (#!1 & sel) #c48a4fff
> color (#!1 & sel) #c47f4eff
> color (#!1 & sel) #c4844fff
> color (#!1 & sel) #c49c6cff
> color (#!1 & sel) #c4a572ff
> color (#!1 & sel) #c4aa76ff
> color (#!1 & sel) #c4aa75ff
> color (#!1 & sel) #c4aa74ff
> color (#!1 & sel) #c4ad72ff
> color (#!1 & sel) #c4b072ff
> color (#!1 & sel) #c4b16dff
> color (#!1 & sel) #c49c6bff
> color (#!1 & sel) #c4916dff
> color (#!1 & sel) #c4906dff
> color (#!1 & sel) #c4916dff
> color (#!1 & sel) #c4946dff
> color (#!1 & sel) #c4966dff
> color (#!1 & sel) #c49871ff
> color (#!1 & sel) #c4a27cff
> color (#!1 & sel) #c4a57eff
> color (#!1 & sel) #c4ab82ff
> color (#!1 & sel) #55557fff
> color sel burly wood
> color sel rosy brown
> graphics silhouettes true
> select clear
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> select up
171 atoms, 173 bonds, 20 residues, 2 models selected
> select up
3184 atoms, 3227 bonds, 445 residues, 2 models selected
> color sel honeydew
> select clear
> select up
12 atoms, 12 bonds, 1 residue, 2 models selected
> select up
140 atoms, 142 bonds, 22 residues, 2 models selected
> select up
3199 atoms, 3234 bonds, 454 residues, 2 models selected
> color sel bisque
> color sel cornsilk
> select clear
> silhouettes color gray
Unknown command: silhouettes color gray
> graphics silhouettes color gray
> graphics silhouettes color maroon
> graphics silhouettes color dim gray
> graphics silhouettes color dimgray black
Expected a keyword
> graphics silhouettes color black
> graphics silhouettes with 0.5
Expected true or false or a keyword
> graphics silhouettes width 0.5
> graphics silhouettes width 1
> graphics silhouettes depthJump 0.05
> graphics silhouettes depthJump 0.01
> graphics silhouettes depthJump 0.03
> select clear
> select /C:49
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
189 atoms, 192 bonds, 27 residues, 2 models selected
> select up
3282 atoms, 3314 bonds, 463 residues, 2 models selected
> color sel white
> select clear
> lighting model options intensity 0.5
Missing or invalid "models" argument: invalid models specifier
> lighting model intensity 0.5
Missing or invalid "models" argument: invalid models specifier
> lighting model intensity 0.5
Missing or invalid "models" argument: invalid models specifier
> lighting intensity 0.5
> lighting intensity 1
> lighting intensity 0.1
> lighting intensity 0.05
> lighting intensity 0.01
> lighting soft
> lighting soft
> lighting full
> lighting soft
> select /B:49@CB
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 2 models selected
> select up
140 atoms, 142 bonds, 22 residues, 2 models selected
> select up
3199 atoms, 3234 bonds, 454 residues, 2 models selected
> color sel azure
> color sel alice blue
> color sel azure
> color sel mint cream
> color sel lavender blush
> color sel seashell
> color sel bisque
> color sel light cyan
> color sel azure
> color sel seashell
> color sel cornsilk
> select clear
> select :106
28 atoms, 24 bonds, 4 residues, 1 model selected
> color sel tomato
> select :81
21 atoms, 18 bonds, 3 residues, 1 model selected
> color sel tomato
> select clear
> select /B:71@CA
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 2 models selected
> select up
35 atoms, 37 bonds, 4 residues, 2 models selected
> select up
3199 atoms, 3234 bonds, 454 residues, 2 models selected
> color sel honeydew
> select clear
> select up
5 atoms, 4 bonds, 1 residue, 2 models selected
> select up
163 atoms, 171 bonds, 22 residues, 2 models selected
> select up
3184 atoms, 3227 bonds, 445 residues, 2 models selected
> color sel cornsilk
> select :81
21 atoms, 18 bonds, 3 residues, 1 model selected
> color sel coral
> color sel tomato
> select :105
23 atoms, 18 bonds, 5 residues, 1 model selected
> color sel tomato
> select clear
> select up
189 atoms, 192 bonds, 27 residues, 2 models selected
> select up
3282 atoms, 3314 bonds, 463 residues, 2 models selected
> color sel dim gray
> color sel dark gray
> select clear
> select up
189 atoms, 192 bonds, 27 residues, 2 models selected
> select up
3282 atoms, 3314 bonds, 463 residues, 2 models selected
> color sel saddle brown
> color sel brown
> color sel rosy brown
> color (#!1 & sel) #dcecf9ff
> color (#!1 & sel) #ccccccff
> color (#!1 & sel) #adadadff
> color (#!1 & sel) #00005aff
> color (#!1 & sel) #e1e1e1ff
> color (#!1 & sel) #adadadff
> color (#!1 & sel) #bc8f8fff
> color (#!1 & sel) #bc9191ff
> color (#!1 & sel) #bc9696ff
> color (#!1 & sel) #bc9898ff
> color (#!1 & sel) #bca09fff
> color (#!1 & sel) #bca8a6ff
> color (#!1 & sel) #bca9a7ff
> color (#!1 & sel) #bcadaaff
> color (#!1 & sel) #bbaca9ff
> color (#!1 & sel) #a99b99ff
> color (#!1 & sel) #a59795ff
> color (#!1 & sel) #a09390ff
> color (#!1 & sel) #a0928fff
> color (#!1 & sel) #a08e8bff
> color (#!1 & sel) #a08d8aff
> color (#!1 & sel) #a08c89ff
> color (#!1 & sel) #a18d8aff
> color (#!1 & sel) #a6918fff
> color (#!1 & sel) #a7928fff
> color (#!1 & sel) #a99491ff
> color (#!1 & sel) #a9948fff
> color (#!1 & sel) #a99693ff
> color (#!1 & sel) #a99895ff
> color (#!1 & sel) #a99795ff
> color (#!1 & sel) #aa9896ff
> color (#!1 & sel) #a99795ff
> color (#!1 & sel) #a69493ff
> color (#!1 & sel) #a59392ff
> color (#!1 & sel) #a49291ff
> color (#!1 & sel) #a2918fff
> color (#!1 & sel) #9d8c8bff
> color (#!1 & sel) #9c8b8aff
> color (#!1 & sel) #9b8a89ff
> select clear
> graphics shilouettes color white
Expected a keyword
> graphics shihlouettes color white
Expected a keyword
> graphics silhouettes color white
> graphics silhouettes color black
> select up
189 atoms, 192 bonds, 27 residues, 2 models selected
> select up
3282 atoms, 3314 bonds, 463 residues, 2 models selected
> color (#!1 & sel) #ffffffff
> select clear
> select :106
28 atoms, 24 bonds, 4 residues, 1 model selected
> color sel tomato
> select :81
21 atoms, 18 bonds, 3 residues, 1 model selected
> color sel tomato
> select clear
> save P:/PcTx_manuscript/VCFstructure.cxs
> select up
5 atoms, 4 bonds, 1 residue, 2 models selected
> select up
163 atoms, 171 bonds, 22 residues, 2 models selected
> select up
3184 atoms, 3227 bonds, 445 residues, 2 models selected
> ui tool show "Color Actions"
> color sel azure
> color sel pale turquoise
> color sel light cyan
> select clear
> save P:/PcTx_manuscript/Fig2_structureChimX.png width 636 height 340
> supersample 3
> save P:/PcTx_manuscript/Fig2_structureChimX.jpg width 636 height 340
> supersample 3
> save C:\Users\zck761\Desktop\image1.png supersample 3
> 0000
Unknown command: 0000
> save C:\Users\zck761\Desktop\image2.png supersample 3
> select :106
28 atoms, 24 bonds, 4 residues, 1 model selected
> ui tool show "Color Actions"
> color sel tomato
> select :81
21 atoms, 18 bonds, 3 residues, 1 model selected
> color sel tomato
> select clear
> select up
5 atoms, 4 bonds, 1 residue, 2 models selected
> select up
163 atoms, 171 bonds, 22 residues, 2 models selected
> color sel light cyan
> select clear
> select clear
> select /B:71@CA
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 2 models selected
> select up
35 atoms, 37 bonds, 4 residues, 2 models selected
> select up
3199 atoms, 3234 bonds, 454 residues, 2 models selected
> color sel honeydew
> hide sel surfaces
> color sel medium aquamarine
> color sel rosy brown
> select clear
> select up
5 atoms, 4 bonds, 1 residue, 2 models selected
> select up
163 atoms, 171 bonds, 22 residues, 2 models selected
> select up
3184 atoms, 3227 bonds, 445 residues, 2 models selected
> hide sel surfaces
> color sel light yellow
> color sel honeydew
> select clear
> select up
189 atoms, 192 bonds, 27 residues, 2 models selected
> select up
3282 atoms, 3314 bonds, 463 residues, 2 models selected
> color sel pale green
> color sel rosy brown
> color (#!1 & sel) #dcecf9ff
> color (#!1 & sel) #ccccccff
> color (#!1 & sel) #e1e1e1ff
> color (#!1 & sel) #c1e1e1ff
> color (#!1 & sel) #e1e1e1ff
> color (#!1 & sel) #bc8f8fff
> color (#!1 & sel) #bc9391ff
> color (#!1 & sel) #bc9796ff
> color (#!1 & sel) #bc9897ff
> color (#!1 & sel) #bc9998ff
> color (#!1 & sel) #bf9c9aff
> color (#!1 & sel) #c39f9eff
> color (#!1 & sel) #c9a4a3ff
> color (#!1 & sel) #cea8a7ff
> color (#!1 & sel) #cea7a6ff
> color (#!1 & sel) #cea8a7ff
> color (#!1 & sel) #cea9a7ff
> color (#!1 & sel) #cea9a8ff
> color (#!1 & sel) #ceacabff
> color (#!1 & sel) #ceadabff
> color (#!1 & sel) #ceafacff
> select clear
> select up
140 atoms, 142 bonds, 22 residues, 2 models selected
> select up
3199 atoms, 3234 bonds, 454 residues, 2 models selected
> color (#!1 & sel) #aaaa7fff
> color (#!1 & sel) #aaa783ff
> color (#!1 & sel) #aaa889ff
> color (#!1 & sel) #aaa98bff
> color (#!1 & sel) #aaaa90ff
> color (#!1 & sel) #aaaa95ff
> color (#!1 & sel) #aaa999ff
> color (#!1 & sel) #aaa799ff
> color (#!1 & sel) #aaa898ff
> color (#!1 & sel) #aaa997ff
> color (#!1 & sel) #a8aa94ff
> color (#!1 & sel) #a8aa8dff
> color (#!1 & sel) #a7aa8cff
> color (#!1 & sel) #a5aa8bff
> color (#!1 & sel) #a2a788ff
> color (#!1 & sel) #afb493ff
> color (#!1 & sel) #b4ba98ff
> color (#!1 & sel) #bec4a0ff
> color (#!1 & sel) #bbc4a4ff
> color (#!1 & sel) #b9c4a4ff
> color (#!1 & sel) #b7c4a2ff
> color (#!1 & sel) #b2c49eff
> color (#!1 & sel) #b2c49fff
> color (#!1 & sel) #b4c4a2ff
> color (#!1 & sel) #b5c5a2ff
> color (#!1 & sel) #c0d1acff
> color (#!1 & sel) #c4d5b0ff
> color (#!1 & sel) #cbddb6ff
> select clear
> select up
142 atoms, 142 bonds, 26 residues, 2 models selected
> select up
3184 atoms, 3227 bonds, 445 residues, 2 models selected
> color sel dim gray
> color sel dark gray
> color sel slate gray
> color sel silver
> color (#!1 & sel) #ffffffff
> color (#!1 & sel) #cbddb6ff
> select clear
> select up
189 atoms, 192 bonds, 27 residues, 2 models selected
> select up
3282 atoms, 3314 bonds, 463 residues, 2 models selected
> select clear
> select up
146 atoms, 146 bonds, 24 residues, 2 models selected
> select up
3199 atoms, 3234 bonds, 454 residues, 2 models selected
> select clear
> select clear
> select /A:295
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
163 atoms, 171 bonds, 22 residues, 2 models selected
> select up
3184 atoms, 3227 bonds, 445 residues, 2 models selected
> color (#!1 & sel) #ffffffff
> color (#!1 & sel) #d4e8f8ff
> color (#!1 & sel) #f0f0f0ff
> color (#!1 & sel) #a0a0a0ff
> color (#!1 & sel) #e1e1e1ff
> color (#!1 & sel) #bb8e8eff
> color (#!1 & sel) #bb958eff
> color (#!1 & sel) #bb968eff
> color (#!1 & sel) #bb9790ff
> color (#!1 & sel) #bb9895ff
> color (#!1 & sel) #bb9898ff
> color (#!1 & sel) #bb9a9aff
> color (#!1 & sel) #bf9d9dff
> color (#!1 & sel) #d0ababff
> color (#!1 & sel) #d6b0b0ff
> color (#!1 & sel) #d9b3b3ff
> color (#!1 & sel) #d9b5b1ff
> color (#!1 & sel) #d9b8b5ff
> color (#!1 & sel) #d9bab7ff
> color (#!1 & sel) #d9bdbbff
> color (#!1 & sel) #d9c1bfff
> color (#!1 & sel) #d9c1c0ff
> color (#!1 & sel) #d9c0bfff
> color (#!1 & sel) #d9c1bfff
> color (#!1 & sel) #d9c3bfff
> color (#!1 & sel) #d9c1bfff
> color (#!1 & sel) #d9c0bfff
> color (#!1 & sel) #d9c1c0ff
> color (#!1 & sel) #d9c1c1ff
> color (#!1 & sel) #d9c3c2ff
> color (#!1 & sel) #d9c4c3ff
> color (#!1 & sel) #d9c6c5ff
> color (#!1 & sel) #d9c8c7ff
> color (#!1 & sel) #d9c7c7ff
> color (#!1 & sel) #d9bfbfff
> color (#!1 & sel) #dac0c0ff
> color (#!1 & sel) #d1b8b8ff
> color (#!1 & sel) #ceb5b5ff
> color (#!1 & sel) #d0b7b7ff
> color (#!1 & sel) #d3babaff
> select clear
> select up
189 atoms, 192 bonds, 27 residues, 2 models selected
> select up
3282 atoms, 3314 bonds, 463 residues, 2 models selected
> color (#!1 & sel) #ffffffff
> color (#!1 & sel) #d5e8f8ff
> color (#!1 & sel) #f0f0f0ff
> color (#!1 & sel) #c0c0c0ff
> color (#!1 & sel) #c1c1c1ff
> color (#!1 & sel) #bdbdbdff
> color (#!1 & sel) #bcbcbcff
> color (#!1 & sel) #b7b7b7ff
> color (#!1 & sel) #b3b3b3ff
> color (#!1 & sel) #b1b1b1ff
> color (#!1 & sel) #afafafff
> color (#!1 & sel) #adadadff
> color (#!1 & sel) #a9a9a9ff
> color (#!1 & sel) #a4a4a4ff
> color (#!1 & sel) #909090ff
> color (#!1 & sel) #8b8b8bff
> color (#!1 & sel) #878787ff
> color (#!1 & sel) #888888ff
> color (#!1 & sel) #8a8a8aff
> color (#!1 & sel) #8b8b8bff
> color (#!1 & sel) #8c8c8cff
> color (#!1 & sel) #8e8e8eff
> color (#!1 & sel) #919191ff
> select clear
> select up
189 atoms, 192 bonds, 27 residues, 2 models selected
> select up
3282 atoms, 3314 bonds, 463 residues, 2 models selected
> color (#!1 & sel) #939393ff
> color (#!1 & sel) #999999ff
> color (#!1 & sel) #9d9d9dff
> color (#!1 & sel) #a0a0a0ff
> color (#!1 & sel) #a1a1a1ff
> color (#!1 & sel) #a0a0a0ff
> color (#!1 & sel) #9e9e9eff
> select clear
> color #ffffffff
> undo
> select :350
24 atoms, 21 bonds, 3 residues, 1 model selected
> show sel atoms
> color sel orange
> select clear
> select up
7 atoms, 7 bonds, 1 residue, 2 models selected
> select up
23 atoms, 23 bonds, 3 residues, 2 models selected
> select up
307 atoms, 313 bonds, 43 residues, 2 models selected
> hide sel surfaces
Drag select of 4fz0.cif_M SES surface, 1351 of 43718 triangles, 30 residues
> cartoon style radius auto
> cartoon style width auto
Invalid "width" argument: Expected a number
> cartoon style width 2
> cartoon style width 2
> select clear
> select up
163 atoms, 171 bonds, 22 residues, 2 models selected
> select up
3199 atoms, 3234 bonds, 454 residues, 2 models selected
> select up
10557 atoms, 10686 bonds, 1486 residues, 2 models selected
> select up
10557 atoms, 10686 bonds, 1486 residues, 7 models selected
> select up
10557 atoms, 10686 bonds, 1486 residues, 7 models selected
> select up
10557 atoms, 10686 bonds, 1486 residues, 7 models selected
> select up
10557 atoms, 10686 bonds, 1486 residues, 7 models selected
> select up
10557 atoms, 10686 bonds, 1486 residues, 7 models selected
> cartoon style width 2
> cartoon style thickness 0.4
> cartoon style thickness 0.6
> cartoon style thickness 0.6
> cartoon style thickness 0.8
> select clear
> select up
171 atoms, 173 bonds, 20 residues, 2 models selected
> select up
3199 atoms, 3234 bonds, 454 residues, 2 models selected
> select up
10557 atoms, 10686 bonds, 1486 residues, 2 models selected
> select up
10557 atoms, 10686 bonds, 1486 residues, 7 models selected
> select up
10557 atoms, 10686 bonds, 1486 residues, 7 models selected
> select up
10557 atoms, 10686 bonds, 1486 residues, 7 models selected
> hide sel atoms
> select :351
33 atoms, 33 bonds, 3 residues, 1 model selected
> select clear
> color sel honeydew
> select clear
> color hot pink
> undo
> color (#!1 & sel) #cbddb6ff
> select /C:217
8 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!1 & sel) #d3babaff
> color sel dark gray
> select clear
> select :351
33 atoms, 33 bonds, 3 residues, 1 model selected
> show sel atoms
> color sel orange
> style sel stick
Changed 33 atom styles
> select clear
> preset cartoons/nucleotides ribbons/slabs
Changed 10439 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
> undo
> select up
212 atoms, 218 bonds, 27 residues, 4 models selected
> select up
892 atoms, 911 bonds, 124 residues, 4 models selected
> show sel surfaces
> select clear
> select up
288 atoms, 290 bonds, 39 residues, 3 models selected
> select up
6466 atoms, 6541 bonds, 908 residues, 3 models selected
> select clear
> select /A:141
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
99 atoms, 98 bonds, 12 residues, 2 models selected
> select up
3184 atoms, 3227 bonds, 445 residues, 2 models selected
> ui tool show "Color Actions"
> color sel light blue
> color sel light steel blue
> select clear
> select up
99 atoms, 98 bonds, 12 residues, 2 models selected
> select up
3184 atoms, 3227 bonds, 445 residues, 2 models selected
> color sel khaki
> color sel pale goldenrod
> color sel light goldenrod yellow
> color sel lemon chiffon
> select clear
> select up
99 atoms, 98 bonds, 12 residues, 2 models selected
> select up
3184 atoms, 3227 bonds, 445 residues, 2 models selected
> color sel light cyan
> select clear
> select up
99 atoms, 98 bonds, 12 residues, 2 models selected
> select up
3184 atoms, 3227 bonds, 445 residues, 2 models selected
> color sel pale turquoise
> select clear
> select up
85 atoms, 86 bonds, 13 residues, 2 models selected
> select up
3184 atoms, 3227 bonds, 445 residues, 2 models selected
> color sel light gray
> select clear
> select up
87 atoms, 86 bonds, 12 residues, 2 models selected
> select up
3282 atoms, 3314 bonds, 463 residues, 2 models selected
> color sel powder blue
> color sel silver
> color sel light steel blue
> color sel dim gray
> select clear
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> select clear
> undo
> undo
> undo
> undo
> undo
> select clear
> select up
85 atoms, 86 bonds, 13 residues, 2 models selected
> select up
3184 atoms, 3227 bonds, 445 residues, 2 models selected
> color (#!1 & sel) #cbddb6ff
> color (#!1 & sel) #d3babaff
> select clear
> select up
39 atoms, 38 bonds, 8 residues, 2 models selected
> select up
3184 atoms, 3227 bonds, 445 residues, 2 models selected
> color sel slate gray
> color sel dim gray
> color sel medium slate blue
> color sel dim gray
> color sel slate gray
> select clear
> select up
142 atoms, 142 bonds, 26 residues, 2 models selected
> select up
3184 atoms, 3227 bonds, 445 residues, 2 models selected
> color (#!1 & sel) #cbddb6ff
> select clear
> undo
> undo
> undo
> undo
> select clear
> select up
189 atoms, 192 bonds, 27 residues, 2 models selected
> select up
3282 atoms, 3314 bonds, 463 residues, 2 models selected
> color sel slate gray
> select up
3367 atoms, 3400 bonds, 476 residues, 3 models selected
> select up
6466 atoms, 6541 bonds, 908 residues, 3 models selected
> color sel navajo white
> undo
> select clear
> select /A:63
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
85 atoms, 86 bonds, 13 residues, 2 models selected
> select up
3184 atoms, 3227 bonds, 445 residues, 2 models selected
> color sel wheat
> color sel light gray
> select clear
> select up
99 atoms, 98 bonds, 12 residues, 2 models selected
> select up
3184 atoms, 3227 bonds, 445 residues, 2 models selected
> color sel misty rose
> color sel rosy brown
> color (#!1 & sel) #d3babaff
> select clear
> select clear
> select /B:355
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
91 atoms, 92 bonds, 12 residues, 2 models selected
> color (#!1 & sel) #cbddb6ff
> select clear
> select up
150 atoms, 150 bonds, 19 residues, 2 models selected
> select up
3282 atoms, 3314 bonds, 463 residues, 2 models selected
> color (#!1 & sel) #ffffffff
> select clear
> undo
> undo
> undo
> select clear
> select clear
> select up
163 atoms, 171 bonds, 22 residues, 2 models selected
> select up
3184 atoms, 3227 bonds, 445 residues, 2 models selected
> color sel pale turquoise
> select clear
> lighting soft
> lighting full
> lighting simple
> lighting flat
> lighting soft
> select clear
> save P:/PcTx_manuscript/Fig1.cxs
opened ChimeraX session
> windowsize
window size 671 492
> windowsize 900
QWindowsWindow::setGeometry: Unable to set geometry 2149x1137-1920-293 (frame:
2165x1176-1928-324) on QWidgetWindow/"MainWindowClassWindow" on
"\\\\.\DISPLAY2". Resulting geometry: 1920x1137-1920-293 (frame:
1936x1176-1928-324) margins: 8, 31, 8, 8 minimum size: 288x258 MINMAXINFO
maxSize=0,0 maxpos=0,0 mintrack=304,297 maxtrack=0,0)
> windowsize 1800
QWindowsWindow::setGeometry: Unable to set geometry 3163x1137-1920-293 (frame:
3179x1176-1928-324) on QWidgetWindow/"MainWindowClassWindow" on
"\\\\.\DISPLAY2". Resulting geometry: 1920x1137-1920-293 (frame:
1936x1176-1928-324) margins: 8, 31, 8, 8 minimum size: 288x258 MINMAXINFO
maxSize=0,0 maxpos=0,0 mintrack=304,297 maxtrack=0,0)
> windowsize 1800 120
> windowsize default
Expected an integer >= 1 or a keyword
> windowsize 800
> windowsize 600
> windowsize 400
> windowsize 800
QWindowsWindow::setGeometry: Unable to set geometry 2049x1137-1920-293 (frame:
2065x1176-1928-324) on QWidgetWindow/"MainWindowClassWindow" on
"\\\\.\DISPLAY2". Resulting geometry: 1920x1137-1920-293 (frame:
1936x1176-1928-324) margins: 8, 31, 8, 8 minimum size: 288x258 MINMAXINFO
maxSize=0,0 maxpos=0,0 mintrack=304,297 maxtrack=0,0)
> windowsize 1800
QWindowsWindow::setGeometry: Unable to set geometry 3113x1137-1920-293 (frame:
3129x1176-1928-324) on QWidgetWindow/"MainWindowClassWindow" on
"\\\\.\DISPLAY2". Resulting geometry: 1920x1137-1920-293 (frame:
1936x1176-1928-324) margins: 8, 31, 8, 8 minimum size: 288x258 MINMAXINFO
maxSize=0,0 maxpos=0,0 mintrack=304,297 maxtrack=0,0)
> save highres width 900 height 500 supersample 3
Cannot determine format for 'highres'
> save highres format png width 900 height 500 supersample 3
Unknown data format: 'png'
> save highres [format png] [width 900] [height 500] [supersample 3]
Cannot determine format for 'highres'
> save highres [png] [900] [500] [supersample 3]
Cannot determine format for 'highres'
> save highres png 900 500 supersample 3
Cannot determine format for 'highres'
> save highres.png 900 500 supersample 3
Expected a keyword
> save highres.png width 900 height 500 supersample 3
> save P:/PcTx_manuscript/highres.png width 900 height 500 supersample 3
> save P:/PcTx_manuscript/highres.png width 900 height 800 supersample 3
> save P:/PcTx_manuscript/highres.png width 900 height 800 pixlesize 0.4
> supersample 3
Expected a keyword
> save P:/PcTx_manuscript/highres.png width 900 height 800 pixlesize 0.2
> supersample 3
Expected a keyword
> save P:/PcTx_manuscript/highres.png width 900 height 800 pixelSize 0.2
> supersample 3
Cannot specify width or height if pixel_size is given
> save P:/PcTx_manuscript/highres.png pixelSize 0.2 supersample 3
> save P:/PcTx_manuscript/highres.png width 1000 height 900 supersample 4
> save P:/PcTx_manuscript/highres.png width 2000 height 1800 supersample 4
> save P:/PcTx_manuscript/Fig1.cxs
——— End of log from Fri Apr 23 19:53:48 2021 ———
opened ChimeraX session
> select add /B:63
5 atoms, 4 bonds, 1 residue, 1 model selected
> undo
> select /B:56
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:427
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add /B:57
10 atoms, 8 bonds, 2 residues, 2 models selected
> select up
171 atoms, 173 bonds, 26 residues, 3 models selected
> select up
6383 atoms, 6461 bonds, 899 residues, 3 models selected
> show sel surfaces
> select clear
> select add /A:366@CB
1 atom, 1 residue, 1 model selected
> select add /B:68@CD1
2 atoms, 2 residues, 2 models selected
> select up
18 atoms, 17 bonds, 2 residues, 3 models selected
> select up
224 atoms, 227 bonds, 33 residues, 3 models selected
> select up
6383 atoms, 6461 bonds, 899 residues, 3 models selected
> select clear
> select add /A:367@ND2
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
105 atoms, 105 bonds, 13 residues, 2 models selected
> select up
3184 atoms, 3227 bonds, 445 residues, 2 models selected
> ui tool show "Color Actions"
> color sel powder blue
> color sel light blue
> color sel light blue
> color sel light steel blue
> color sel light cyan
> select clear
> select add /B:45@O
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 4 bonds, 1 residue, 2 models selected
> select up
15 atoms, 14 bonds, 3 residues, 2 models selected
> select up
3199 atoms, 3234 bonds, 454 residues, 2 models selected
> select up
10557 atoms, 10686 bonds, 1486 residues, 2 models selected
> select down
3199 atoms, 3234 bonds, 454 residues, 7 models selected
> color sel light goldenrod yellow
> color sel honeydew
> color sel lemon chiffon
> color sel beige
> color sel honeydew
> color sel honeydew
> color sel lemon chiffon
> color sel light goldenrod yellow
> color (#!1 & sel) #fdfffcff
> color (#!1 & sel) #fdfffcff
> color (#!1 & sel) #fafff6ff
> color (#!1 & sel) #f6ffeeff
> color (#!1 & sel) #f3ffe8ff
> color (#!1 & sel) #f1ffe4ff
> color (#!1 & sel) #efffe1ff
> color (#!1 & sel) #efffdfff
> color (#!1 & sel) #eeffdeff
> color (#!1 & sel) #ecffddff
> color (#!1 & sel) #e9ffddff
> color (#!1 & sel) #e7ffddff
> color (#!1 & sel) #e5ffdcff
> color (#!1 & sel) #e5ffddff
> color (#!1 & sel) #e5ffddff
> color (#!1 & sel) #e5ffdeff
> color (#!1 & sel) #e6ffdeff
> select clear
> ui tool show "Side View"
> save "/Users/zck761/Google Drive/My Drive/PLESS_LAB/Labpics/ASIC1-PcTx1.cxs"
——— End of log from Fri Apr 22 15:36:01 2022 ———
opened ChimeraX session
> close session
> load 4FZ0
Unknown command: load 4FZ0
> open 4FZ0
Summary of feedback from opening 4FZ0 fetched from pdb
---
notes | Fetching compressed mmCIF 4fz0 from
http://files.rcsb.org/download/4fz0.cif
Fetching CCD CL from http://ligand-expo.rcsb.org/reports/C/CL/CL.cif
Fetching CCD GOL from http://ligand-expo.rcsb.org/reports/G/GOL/GOL.cif
4fz0 title:
Crystal structure of acid-sensing ion channel in complex with psalmotoxin 1 at
low pH [more info...]
Chain information for 4fz0 #1
---
Chain | Description
A B C | Acid-sensing ion channel 1
M N O | Pi-theraphotoxin-Pc1a
Non-standard residues in 4fz0 #1
---
CL — chloride ion
GOL — glycerol (glycerin; propane-1,2,3-triol)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose
> select /C:427@CG2
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
157 atoms, 157 bonds, 24 residues, 1 model selected
> select up
3282 atoms, 3314 bonds, 463 residues, 1 model selected
> select up
10557 atoms, 10686 bonds, 1486 residues, 1 model selected
> select up
10557 atoms, 10686 bonds, 1486 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> preset cartoons/nucleotides cylinders/stubs
Changed 10328 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
> cartoon style width 1.5 thickness 0.3
> cartoon style width 1.5 thickness 0.5
> cartoon style width 1.5 thickness 0.7
> cartoon style width 1.5 thickness 1
> cartoon style width 2
> cartoon style width 4
> cartoon style width 2
> cartoon style arrows false
> cartoon style coil with 0.5
Expected a keyword
> cartoon style coil width 0'.5
Invalid "width" argument: Expected a number
> cartoon style coil width 0.5
> cartoon style coil width 1
> cartoon style width 0.5
> cartoon style coil thickness 0.6
> preset cartoons/nucleotides cylinders/stubs
Changed 10328 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
> lighting shadows false
> select clear
> select add /B:63
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
140 atoms, 142 bonds, 22 residues, 1 model selected
> select up
3199 atoms, 3234 bonds, 454 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #e6ffdeff
> select clear
> select add /A:294
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
163 atoms, 171 bonds, 22 residues, 1 model selected
> select up
3184 atoms, 3227 bonds, 445 residues, 1 model selected
> color sel light cyan
> select clear
> select add /C:59
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
189 atoms, 192 bonds, 27 residues, 1 model selected
> select up
3282 atoms, 3314 bonds, 463 residues, 1 model selected
> color sel dark gray
> color sel dark slate gray
> color sel slate gray
> select clear
> select /M:22
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add /N:10
15 atoms, 13 bonds, 2 residues, 1 model selected
> select subtract /N:10
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add /N:10
15 atoms, 13 bonds, 2 residues, 1 model selected
> select add /O:22
24 atoms, 21 bonds, 3 residues, 1 model selected
> select up
212 atoms, 218 bonds, 27 residues, 1 model selected
> select up
892 atoms, 911 bonds, 124 residues, 1 model selected
> color sel teal
> color sel dark cyan
> select add /B:58
900 atoms, 918 bonds, 125 residues, 1 model selected
> select add /A:430
908 atoms, 925 bonds, 126 residues, 1 model selected
> select up
1174 atoms, 1195 bonds, 172 residues, 1 model selected
> select up
7275 atoms, 7372 bonds, 1023 residues, 1 model selected
> show sel surfaces
> undo
> undo
> undo
> select clear
> select add /B:425@CE2
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 2 models selected
> select up
17 atoms, 17 bonds, 2 residues, 2 models selected
> select up
3199 atoms, 3234 bonds, 454 residues, 2 models selected
> hide sel surfaces
> select up
10557 atoms, 10686 bonds, 1486 residues, 2 models selected
> select up
10557 atoms, 10686 bonds, 1486 residues, 6 models selected
> select up
10557 atoms, 10686 bonds, 1486 residues, 6 models selected
> hide sel surfaces
> ui tool show "Color Actions"
> show sel surfaces
> hide sel surfaces
> select clear
> lighting soft
> select /B:54
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
140 atoms, 142 bonds, 22 residues, 2 models selected
> select up
3199 atoms, 3234 bonds, 454 residues, 2 models selected
> surface (#!1 & sel)
> ui tool show "Color Actions"
> color sel honeydew
> color (#!1 & sel) #e6ffdeff
> color (#!1 & sel) #e6ffdeff
> select clear
> select add /A:155
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
84 atoms, 85 bonds, 10 residues, 2 models selected
> select up
3184 atoms, 3227 bonds, 445 residues, 2 models selected
> show sel surfaces
> color sel light cyan
> select clear
> select add /A:205@NZ
1 atom, 1 residue, 1 model selected
> select clear
> select /M:21
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /O:33
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add /N:14
16 atoms, 15 bonds, 2 residues, 1 model selected
> select add /M:22
25 atoms, 23 bonds, 3 residues, 2 models selected
> select up
202 atoms, 207 bonds, 27 residues, 3 models selected
> select up
892 atoms, 911 bonds, 124 residues, 4 models selected
> surface (#!1 & sel)
> color sel teal
> color sel dark cyan
> transparency (#!1 & sel) 80
> transparency (#!1 & sel) 30
> select clear
> ui tool show "Side View"
> save "/Volumes/GoogleDrive/My Drive/PLESS_LAB/Labpics/ASIC1-PcTx1_DS.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 609, in closeEvent
sbar.destroy()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/statusbar.py", line 51, in destroy
v.delete()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 438, in delete
self.make_current()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 478, in make_current
return self._opengl_context.make_current()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 99, in make_current
qc = self._initialize_context()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 125, in _initialize_context
qc.setScreen(self._screen)
RuntimeError: wrapped C/C++ object of type QScreen has been deleted
RuntimeError: wrapped C/C++ object of type QScreen has been deleted
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 125, in _initialize_context
qc.setScreen(self._screen)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/sideview/tool.py", line 112, in _redraw
self.render()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/sideview/tool.py", line 142, in render
mvwin = self.view.render.use_shared_context(self)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 524, in use_shared_context
self.make_current()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 478, in make_current
return self._opengl_context.make_current()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 108, in make_current
raise OpenGLError("Could not make graphics context current")
chimerax.graphics.opengl.OpenGLError: Could not make graphics context current
Error processing trigger "frame drawn":
chimerax.graphics.opengl.OpenGLError: Could not make graphics context current
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 108, in make_current
raise OpenGLError("Could not make graphics context current")
See log for complete Python traceback.
OpenGL version: unknown
Could not make opengl context currentHardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Processor Name: Unknown
Processor Speed: 2,4 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache: 8 MB
Memory: 16 GB
Software:
System Software Overview:
System Version: macOS 12.3.1 (21E258)
Kernel Version: Darwin 21.4.0
Time since boot: 20 days 19:22
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
S24E650:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.5.0
chardet: 3.0.4
ChimeraX-AddCharge: 1.0.1
ChimeraX-AddH: 2.1.6
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.13.2
ChimeraX-AtomicLibrary: 3.1.3
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.4
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.5
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.3
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: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.2.1
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.1
ChimeraX-ModelPanel: 1.0.1
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: 2.0.1
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3.1
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: 1.0.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7.6
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 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: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 5.0.9
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 2.0.1
matplotlib: 3.3.2
matplotlib-inline: 0.1.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.18
psutil: 5.7.2
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
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: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.3.0
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
