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#5728 closed defect (not a bug)
morph rate/ramp syntax
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Comparison | Version: | |
| Keywords: | Cc: | Elaine Meng | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.3rc202111110135 (2021-11-11 01:35:07 UTC)
Description
Error with syntax for "moprh" command. When I type "morph #4,3 rate ramp up" I get the error: "Invalid "rate" argument: 'ramp' is ambiguous, could be ramp down, ramp up". However I do not see how to specify it differently?
Log:
UCSF ChimeraX version: 1.3rc202111110135 (2021-11-11)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/Sessions/FigSX__EJC_ALY_interaction_Details_v2.cxs"
> format session
Log from Thu Dec 2 14:18:13 2021UCSF ChimeraX version: 1.3rc202111110135
(2021-11-11)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/Sessions/FigSX__EJC_ALY_interaction_Details_v2.cxs"
Log from Thu Dec 2 11:47:48 2021UCSF ChimeraX version: 1.3rc202111110135
(2021-11-11)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/Sessions/FigSX__EJC_ALY_interaction_Details_v2.cxs"
> format session
Log from Thu Dec 2 11:17:26 2021UCSF ChimeraX version: 1.3rc202111110135
(2021-11-11)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/Sessions/FigSX__EJC_ALY_interaction_Details.cxs"
Log from Wed Dec 1 18:26:32 2021UCSF ChimeraX version: 1.3rc202111110135
(2021-11-11)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/Sessions/FigSX_Clash_EJC_ALY_Spliceosome_U5S1.cxs"
Log from Tue Nov 30 19:11:56 2021UCSF ChimeraX version: 1.3rc202111110135
(2021-11-11)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/Sessions/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_aka_Snu114.cxs"
Log from Tue Nov 30 17:59:19 2021UCSF ChimeraX version: 1.3rc202111110135
(2021-11-11)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 6qdv
6qdv title:
Human post-catalytic P complex spliceosome [more info...]
Chain information for 6qdv #1
---
Chain | Description | UniProt
2 | U2 snRNA |
5 | U5 snRNA |
6 | U6 snRNA |
7 | Eukaryotic initiation factor 4A-III | IF4A3_HUMAN
8 | RNA-binding protein 8A | RBM8A_HUMAN
9 | Protein mago nashi homolog 2 | MGN2_HUMAN
A | Pre-mRNA-processing-splicing factor 8 | PRP8_HUMAN
B | U5 small nuclear ribonucleoprotein 200 kDa helicase | U520_HUMAN
C | 116 kDa U5 small nuclear ribonucleoprotein component | U5S1_HUMAN
D | PRKR-interacting protein 1 | PKRI1_HUMAN
E | Ligated exons: MINX mRNA |
F | Cactin | CATIN_HUMAN
G | Protein FAM32A | FA32A_HUMAN
H | Pre-mRNA-splicing factor CWC22 homolog | CWC22_HUMAN
I | Intron lariat: MINX RNA |
J | Pleiotropic regulator 1 | PLRG1_HUMAN
K | SNW domain-containing protein 1 | SNW1_HUMAN
L | Protein BUD31 homolog | BUD31_HUMAN
M | Pre-mRNA-splicing factor RBM22 | RBM22_HUMAN
N | U5 small nuclear ribonucleoprotein 40 kDa protein | SNR40_HUMAN
O | Cell division cycle 5-like protein | CDC5L_HUMAN
P | Spliceosome-associated protein CWC15 homolog | CWC15_HUMAN
R | Serine/arginine repetitive matrix protein 2 | SRRM2_HUMAN
S | Crooked neck-like protein 1 | CRNL1_HUMAN
T | Pre-mRNA-splicing factor SYF1 | SYF1_HUMAN
U | Intron-binding protein aquarius | AQR_HUMAN
V | ATP-dependent RNA helicase DHX8 | DHX8_HUMAN
W | U2 small nuclear ribonucleoprotein A' | RU2A_HUMAN
Y | U2 small nuclear ribonucleoprotein B'' | RU2B_HUMAN
Z | NF-kappa-B-activating protein | NKAP_HUMAN
b k | Small nuclear ribonucleoprotein-associated proteins B and B' |
RSMB_HUMAN
c | Pre-mRNA-splicing factor SLU7 | SLU7_HUMAN
d n | Small nuclear ribonucleoprotein Sm D3 | SMD3_HUMAN
e p | Small nuclear ribonucleoprotein E | RUXE_HUMAN
f q | Small nuclear ribonucleoprotein F | RUXF_HUMAN
g r | Small nuclear ribonucleoprotein G | RUXG_HUMAN
h l | Small nuclear ribonucleoprotein Sm D1 | SMD1_HUMAN
i | Peptidyl-prolyl cis-trans isomerase-like 1 | PPIL1_HUMAN
j m | Small nuclear ribonucleoprotein Sm D2 | SMD2_HUMAN
o | Pre-mRNA-processing factor 17 | PRP17_HUMAN
s | Pre-mRNA-splicing factor SPF27 | SPF27_HUMAN
t u v w | Pre-mRNA-processing factor 19 | PRP19_HUMAN
y | Pre-mRNA-splicing factor SYF2 | SYF2_HUMAN
z | Replication stress response regulator SDE2 | SDE2_HUMAN
Non-standard residues in 6qdv #1
---
ATP — adenosine-5'-triphosphate
GTP — guanosine-5'-triphosphate
IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol
1,2,3,4,5,6-hexakisphosphate)
K — potassium ion
MG — magnesium ion
ZN — zinc ion
> open "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/pdbs/refine_run4_real_space_refined_noSS.pdb"
Chain information for refine_run4_real_space_refined_noSS.pdb #2
---
Chain | Description
A F K a f k | No description available
B G L b g l | No description available
C H M c h m | No description available
D I N d i n | No description available
E J O e j o | No description available
> mmaker #1/7 to #2/A
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 refine_run4_real_space_refined_noSS.pdb, chain A (#2) with 6qdv,
chain 7 (#1), sequence alignment score = 1886.9
RMSD between 380 pruned atom pairs is 0.402 angstroms; (across all 382 pairs:
0.529)
> hide
> show nucleic
> hide protein|solvent|H
> surface hidePatches
> style (protein|nucleic|solvent) & @@draw_mode=0 stick
Changed 155191 atom styles
> cartoon
> cartoon style modeHelix default arrows true arrowsHelix false arrowScale 2
> width 2 thickness 0.4 sides 12 divisions 20
> cartoon style ~(nucleic|strand) xsection round
> cartoon style (nucleic|strand) xsection rectangle
> cartoon style protein modeHelix tube radius 2.2 sides 24 thickness 1.2
> cartoon style nucleic xsection round width 2 thickness 2
> nucleotides stubs
> lighting shadows false
> lighting soft
> camera ortho
> lighting soft
> graphics silhouettes true width 1
> graphics silhouettes depthJump 0.2
> size #1 pseudobondRadius 0.5
Changed 367 pseudobond radii
> select #1 minimumLength 1
367 pseudobonds, 3 models selected
> hide sel
> set bgColor white
> color #1 silver target abcspf
> hide #1 atoms
> show #1 surfaces
> hide #1/7,8,9 cartoons
> transparency #1 90
> show #1 cartoons
> show #1/C cartoons
> color #1/C #DEE222 target c
> color nucleic black
> hide #1&nucleic surfaces
> color #1 silver target abcspf
> hide #1 atoms
> show #1 surfaces
> hide #1/7,8,9 cartoons
> transparency #1 90
> show #1 cartoons
> show #1/C cartoons
> color #1/C #DEE222 target c
> color nucleic black
> hide #1&nucleic surfaces
> color #2/T purple target abcspf
> color #2/A,a,F,f,K,k #F1D8BC
> color #2/B,b,G,g,L,l #EAA439
> color #2/C,c,H,h,M,m #EB6841
> color #2/D,d,I,i,N,n blueviolet
> color #2/E,e,J,j,O,o #303030
> hide #2 cartoons
> show #2/A,B,C,D,E target c
> color #2/D,d,I,i,N,n #86338B
> hide #2 cartoons,atoms
> nucleotides stubs
> show #2/A,B,C,D,E target c
> view name view1
> show #2/D surfaces
> color #2/D,d,I,i,N,n #86338B target abcspf
> transparency #2/D 50
> transparency #2/D 30
> transparency #1/C 40
> color #1/C #DEE222 target cs
> transparency #1/C 40
> transparency #1/C 50
> transparency #1/C 70
> transparency #1/C 100
> transparency #1/C 90
> transparency #1/C 80
> transparency #2/D 80
> transparency #2/D 50
> view name zoom
> color list all
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
.
> hide #1/7,8,9 cartoons
> ui tool show "Side View"
> lighting flat
> lighting soft
> graphics silhouettes depthJump 0.2
> view name zoom
> view name view 2 20
Expected fewer arguments
> view name view2 20
Expected fewer arguments
> view view2 20
Expected an objects specifier or a view name or a keyword
> view list
Named views: view1, zoom
> view view1
> turn y 180
> windowsize 800 800
> view name view1
> view zoom 20
> view view1
> view zoom
> view view1
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view1.png"
> supersample 4 transparentBackground true pixelSize 0.4
> view zoom
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view_Zoom.png"
> supersample 4 transparentBackground true pixelSize 0.4
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/Sessions/FigSX_Clash_EJC_ALY_Spliceosome_U5S1.cxs"
> nucleotides stubs
> view name zoom
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/Sessions/FigSX_Clash_EJC_ALY_Spliceosome_U5S1.cxs"
> show #2/E atoms
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view_Zoom.png"
> supersample 4 transparentBackground true pixelSize 0.4
> view view1
> show #1&nucleic atoms
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view1.png"
> supersample 4 transparentBackground true pixelSize 0.4
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/Sessions/FigSX_Clash_EJC_ALY_Spliceosome_U5S1.cxs"
> view zoom
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view_Zoom.png"
> supersample 4 transparentBackground true pixelSize 0.4
> view view1
> windoswsize 800 800
Unknown command: windoswsize 800 800
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view1.png"
> supersample 4 transparentBackground true pixelSize 0.2
> view zoom
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view_Zoom.png"
> supersample 4 transparentBackground true pixelSize 0.2
> lighting flat
> view view1 50
> select clear
> lighting soft
> lighting shadows false
> lighting soft intensity 0.2 fillIntensity 0.5 ambientIntensity 1
> lighting soft
> lighting flat
> view matrix camera
> -0.96806,-0.2507,-0.0041736,163.16,0.25072,-0.96805,-0.0048718,165.35,-0.0028215,-0.0057607,0.99998,908.84
> turn x 90
[Repeated 1 time(s)]
> hide #!1 models
> view matrix camera
> -0.96806,-0.2507,-0.0041736,163.16,0.25072,-0.96805,-0.0048718,165.35,-0.0028215,-0.0057607,0.99998,908.84
> turn x 90
[Repeated 3 time(s)]
> view view1
> show #!1 models
> view zoom_2
Expected an objects specifier or a view name or a keyword
> ui tool show "Side View"
> view name zoom_2
> lighting soft
> transparency #1/C 80
> transparency #1/C 100
> lighting shadows false
> transparency #1/C 80
> zoom
Pixel size at center of rotation is 0.194
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view_Zoom_2.png"
> supersample 4 transparentBackground true pixelSize 0.2
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/Sessions/FigSX_Clash_EJC_ALY_Spliceosome_U5S1.cxs"
> graphics silhouettes depthJump 0.2
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view_Zoom_2.png"
> supersample 4 transparentBackground true pixelSize 0.2
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/Sessions/FigSX_Clash_EJC_ALY_Spliceosome_U5S1.cxs"
> hide #!1 models
> show #!1 models
> view name zoom_2
> view zoom_2
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view_Zoom_2.png"
> supersample 4 transparentBackground true pixelSize 0.2
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/Sessions/FigSX_Clash_EJC_ALY_Spliceosome_U5S1.cxs"
——— End of log from Tue Nov 30 17:59:19 2021 ———
opened ChimeraX session
> show #2/D,d,I cartoons
> show #2/D,d,I surfaces
> color #2/D,d,I,i,N,n #86338B target abcspf
> ui tool show "Side View"
> size #1 pseudobondRadius 0.5
Changed 367 pseudobond radii
> select #1 minimumLength 1
367 pseudobonds, 3 models selected
> hide sel
> hide #2/I surfaces
> hide #2/d surfaces
> transparency #2/d 50 target c
> hide 2/I c
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide 2/I c
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide 2/I target c
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide 2/I cartoons
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide 2/I ribbons
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #2/I cartoons
> show #2,i c
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #2/i cartoons
> hide #2/i cartoons
> hide #2/N cartoons
> show #2/N cartoons
> transparency #2/D 80
> view zoom_2
> transparency #2/N 20 target c
> show #2/d,N surfaces
> color #2/D,d,I,i,N,n #86338B target abcspf
> transparency #2/D 80
> transparency #2/d 100
> transparency #2/N 100
> transparency #2/N 0 target c
> transparency #2/d 0 target c
> size #1 pseudobondRadius 0.5
Changed 367 pseudobond radii
> select #1 minimumLength 1
367 pseudobonds, 3 models selected
> hide sel
> ~pseudobonds
Unknown command: ~pseudobonds
> size #1 pseudobondRadius 0.5
Changed 367 pseudobond radii
> select #1 minimumLength 1
367 pseudobonds, 3 models selected
> hide sel
> size #2 pseudobondRadius 0.5
Changed 12 pseudobond radii
> select #2 minimumLength 1
12 pseudobonds, 2 models selected
> hide sel
> color #2 #deaee1 target c
> color #2/T purple target abcspf
> color #2/A,a,F,f,K,k #F1D8BC target abcspf
> color #2/B,b,G,g,L,l #EAA439 target abcspf
> color #2/C,c,H,h,M,m #EB6841 target abcspf
> color #2/D,d,I,i,N,n #86338B target abcspf
> color #2/d
> color #2/E,e,J,j,O,o #303030 target abcspf
> hide #2 cartoons,atoms
> show #2/A,B,C,D,E target c
> show #2/D,d,N surfaces
> show #2/D,d,N cartoons
> show #2/E atoms
> transparency #2/D 80
> transparency #2/d 100
> transparency #2/N 100
> color #2/d #303030 target c
> color #2/d #deaee1 target c
> color #2/n #e0b4e3 target c
> color #2/d #deaee1 target c
> color #2/n #e0b4e3
> color #2/n #e0b4e3 target c
> transparency #2/D 60
[Repeated 1 time(s)]
> transparency #2/d 80
> transparency #2/N 100
> transparency #2/D 60
> transparency #2/N 80
> transparency #2/d 100
> transparency #2/N 85
> view zoom_2
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view_Zoom_2.png"
> supersample 4 transparentBackground true pixelSize 0.2
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/Sessions/FigSX_Clash_EJC_ALY_Spliceosome_U5S1.cxs"
> show pseudobonds
> hide pseudobonds
> lighting shadows true intensity 0.5
> lighting flat
> view name alt
> view name alt_zoom
> lighting soft
> view alt
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view1_alt.png"
> supersample 4 transparentBackground true pixelSize 0.2
> view alt_zoom
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_zoom_alt.png"
> supersample 4 transparentBackground true pixelSize 0.2
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/Sessions/FigSX_Clash_EJC_ALY_Spliceosome_U5S1.cxs"
Drag select of 2 atoms
> hide sel
Drag select of 1 atoms
> hide se
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide sel
Drag select of 4 atoms
> hide sek
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
Drag select of 1 atoms
> hide sek
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide sel
Drag select of 4 atoms
> hide sel
Drag select of 1 atoms
> hide sel
> view alt
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view1_alt.png"
> supersample 4 transparentBackground true pixelSize 0.2
> view alt_zoom
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_zoom_alt.png"
> supersample 4 transparentBackground true pixelSize 0.2
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/Sessions/FigSX_Clash_EJC_ALY_Spliceosome_U5S1.cxs"
——— End of log from Tue Nov 30 19:11:56 2021 ———
opened ChimeraX session
> color #1/C cornflowerblue target cs
> transparency #1/C 80
> open 6qdv
6qdv title:
Human post-catalytic P complex spliceosome [more info...]
Chain information for 6qdv #3
---
Chain | Description | UniProt
2 | U2 snRNA |
5 | U5 snRNA |
6 | U6 snRNA |
7 | Eukaryotic initiation factor 4A-III | IF4A3_HUMAN
8 | RNA-binding protein 8A | RBM8A_HUMAN
9 | Protein mago nashi homolog 2 | MGN2_HUMAN
A | Pre-mRNA-processing-splicing factor 8 | PRP8_HUMAN
B | U5 small nuclear ribonucleoprotein 200 kDa helicase | U520_HUMAN
C | 116 kDa U5 small nuclear ribonucleoprotein component | U5S1_HUMAN
D | PRKR-interacting protein 1 | PKRI1_HUMAN
E | Ligated exons: MINX mRNA |
F | Cactin | CATIN_HUMAN
G | Protein FAM32A | FA32A_HUMAN
H | Pre-mRNA-splicing factor CWC22 homolog | CWC22_HUMAN
I | Intron lariat: MINX RNA |
J | Pleiotropic regulator 1 | PLRG1_HUMAN
K | SNW domain-containing protein 1 | SNW1_HUMAN
L | Protein BUD31 homolog | BUD31_HUMAN
M | Pre-mRNA-splicing factor RBM22 | RBM22_HUMAN
N | U5 small nuclear ribonucleoprotein 40 kDa protein | SNR40_HUMAN
O | Cell division cycle 5-like protein | CDC5L_HUMAN
P | Spliceosome-associated protein CWC15 homolog | CWC15_HUMAN
R | Serine/arginine repetitive matrix protein 2 | SRRM2_HUMAN
S | Crooked neck-like protein 1 | CRNL1_HUMAN
T | Pre-mRNA-splicing factor SYF1 | SYF1_HUMAN
U | Intron-binding protein aquarius | AQR_HUMAN
V | ATP-dependent RNA helicase DHX8 | DHX8_HUMAN
W | U2 small nuclear ribonucleoprotein A' | RU2A_HUMAN
Y | U2 small nuclear ribonucleoprotein B'' | RU2B_HUMAN
Z | NF-kappa-B-activating protein | NKAP_HUMAN
b k | Small nuclear ribonucleoprotein-associated proteins B and B' |
RSMB_HUMAN
c | Pre-mRNA-splicing factor SLU7 | SLU7_HUMAN
d n | Small nuclear ribonucleoprotein Sm D3 | SMD3_HUMAN
e p | Small nuclear ribonucleoprotein E | RUXE_HUMAN
f q | Small nuclear ribonucleoprotein F | RUXF_HUMAN
g r | Small nuclear ribonucleoprotein G | RUXG_HUMAN
h l | Small nuclear ribonucleoprotein Sm D1 | SMD1_HUMAN
i | Peptidyl-prolyl cis-trans isomerase-like 1 | PPIL1_HUMAN
j m | Small nuclear ribonucleoprotein Sm D2 | SMD2_HUMAN
o | Pre-mRNA-processing factor 17 | PRP17_HUMAN
s | Pre-mRNA-splicing factor SPF27 | SPF27_HUMAN
t u v w | Pre-mRNA-processing factor 19 | PRP19_HUMAN
y | Pre-mRNA-splicing factor SYF2 | SYF2_HUMAN
z | Replication stress response regulator SDE2 | SDE2_HUMAN
Non-standard residues in 6qdv #3
---
ATP — adenosine-5'-triphosphate
GTP — guanosine-5'-triphosphate
IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol
1,2,3,4,5,6-hexakisphosphate)
K — potassium ion
MG — magnesium ion
ZN — zinc ion
> select #3/I:1-167
872 atoms, 971 bonds, 5 pseudobonds, 42 residues, 3 models selected
> hide #!3 models
> set bgColor white
> color #1 silver target abcspf
> hide #1 atoms
> show #1 surfaces
> hide #1/7,8,9 cartoons
> transparency #1 90
> show #1 cartoons
> color #1/C cornflowerblue target cs
> transparency #1/C 80
> color #1/I black
> hide #!2 models
> hide #1/7,8,9 cartoons
> show #!2 models
> color list all
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
.
> color #1/H pink target c
> view list
Named views: alt, alt_zoom, view1, zoom, zoom_2
> view zoom_2
> hdie solvent
Unknown command: hdie solvent
> hide solvent
> view zoom_2
> view zoom
> view zoom_2
> hide #!1 models
> hide metals
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide Mg
Drag select of 1 atoms
[Repeated 1 time(s)]
> hide ANP
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide hetero
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> view zoom_@
Expected an objects specifier or a view name or a keyword
> view zoom_2
> hide #!2.3 models
> show #!2.3 models
> hide #2.4 models
> hide #!2.5 models
> show #!2.5 models
> hide #!2.6 models
> show #!2.6 models
> hide #2.1 models
> show #2.1 models
> hide #2.2 models
> show #2.2 models
> select #2/I:84@C
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> style sel stick
Changed 8 atom styles
> undo
Drag select of 1 atoms
> hide sel
Drag select of 1 atoms
> hide sel
Drag select of 2 atoms
> hide sek
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide sel
Drag select of 1 atoms
> hide se
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide sel
> view zoom_2
> show #!1 models
> color #1/H black target c
> color #1/H pink target c
> color list all
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
.
> color #1/H salmon target c
> color #1/H plum target c
> color #1/H lavender target c
> color #1/H F5C32C target c
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color #1/H #F5C32C target c
> color #1/H #F5C3C2 target c
> color #1/H #F19CBB target c
> view view1
> windoswsize 800 800
Unknown command: windoswsize 800 800
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view1.png"
> supersample 4 transparentBackground true pixelSize 0.2
> view zoom
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view_Zoom.png"
> supersample 4 transparentBackground true pixelSize 0.2
> view zoom_2
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view_Zoom_2.png"
> supersample 4 transparentBackground true pixelSize 0.2
> view alt
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view1_alt.png"
> supersample 4 transparentBackground true pixelSize 0.2
> view alt_zoom
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_zoom_alt.png"
> supersample 4 transparentBackground true pixelSize 0.2
> color #1/C #98c1d9 target cs
> color #1/C #98c1d9 target c,s
Invalid "target" argument: Character ',' is not an allowed target, must be one
of acrsbmpfl
> transparency #1/C 80
> view view1
> windowsize 800 800
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view1.png"
> supersample 4 transparentBackground true pixelSize 0.2
> view zoom
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view_Zoom.png"
> supersample 4 transparentBackground true pixelSize 0.2
> view zoom_2
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view_Zoom_2.png"
> supersample 4 transparentBackground true pixelSize 0.2
> view alt
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view1_alt.png"
> supersample 4 transparentBackground true pixelSize 0.2
> view alt_zoom
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_zoom_alt.png"
> supersample 4 transparentBackground true pixelSize 0.2
> view view1
> show nucleic atoms
> hide nucleic surfaces
> hide #2/e,j,a
> hide #2/e,j,o atoms
> view view1
> windowsize 800 800
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view1.png"
> supersample 4 transparentBackground true pixelSize 0.2
> view zoom
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view_Zoom.png"
> supersample 4 transparentBackground true pixelSize 0.2
> view zoom_2
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view_Zoom_2.png"
> supersample 4 transparentBackground true pixelSize 0.2
> view alt
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view1_alt.png"
> supersample 4 transparentBackground true pixelSize 0.2
> view alt_zoom
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_zoom_alt.png"
> supersample 4 transparentBackground true pixelSize 0.2
> hide #2/e,j,O,U,o atoms
> hide #2/e,j,O,U,J,o atoms
> view view1
> windowsize 800 800
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view1.png"
> supersample 4 transparentBackground true pixelSize 0.2
> view zoom
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view_Zoom.png"
> supersample 4 transparentBackground true pixelSize 0.2
> view zoom_2
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view_Zoom_2.png"
> supersample 4 transparentBackground true pixelSize 0.2
> view alt
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view1_alt.png"
> supersample 4 transparentBackground true pixelSize 0.2
> view alt_zoom
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_zoom_alt.png"
> supersample 4 transparentBackground true pixelSize 0.2
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/Sessions/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_blue.cxs"
> color #1/C #F8DE7E target c,s
Invalid "target" argument: Character ',' is not an allowed target, must be one
of acrsbmpfl
> transparency #1/C 80
> color #1/C #F8DE7E target c,s
Invalid "target" argument: Character ',' is not an allowed target, must be one
of acrsbmpfl
> color #1/C #F8DE7E target cs
> transparency #1/C 80
> view view1
> windowsize 800 800
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view1_yellow.png"
> supersample 4 transparentBackground true pixelSize 0.2
> view zoom
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view_Zoom_yellow.png"
> supersample 4 transparentBackground true pixelSize 0.2
> view zoom_2
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view_Zoom_2_yellow.png"
> supersample 4 transparentBackground true pixelSize 0.2
> view alt
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view1_alt_yellow.png"
> supersample 4 transparentBackground true pixelSize 0.2
> view alt_zoom
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_zoom_alt_yellow.png"
> supersample 4 transparentBackground true pixelSize 0.2
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/Sessions/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_yellow.cxs"
> hide #1/C surfaces
> hide #1/D surfaces
> undo
> hide #2/D surfaces
> show #2/D surfaces
> hide #2/D surfaces
> view view1
> windowsize 800 800
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view1_yellow.png"
> supersample 4 transparentBackground true pixelSize 0.2
> view zoom
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view_Zoom_yellow.png"
> supersample 4 transparentBackground true pixelSize 0.2
> view zoom_2
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view_Zoom_2_yellow.png"
> supersample 4 transparentBackground true pixelSize 0.2
> view alt
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view1_alt_yellow.png"
> supersample 4 transparentBackground true pixelSize 0.2
> view alt_zoom
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_zoom_alt_yellow.png"
> supersample 4 transparentBackground true pixelSize 0.2
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/Sessions/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_yellow.cxs"
> ui tool show "Side View"
> view zoom
> view zoom_2
> hide #1 surfaces
> transparency #1 50 target c
> transparency #1/H,C 0 target c
> transparency #1 80 target c
> transparency #1/H,C 0 target c
> transparency #1 80 target c
> transparency #1/H,C 0 target c
> view view1
> windowsize 800 800
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view_no_surface+1_yellow.png"
> supersample 4 transparentBackground true pixelSize 0.2
> view zoom
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view_Zoom_yellow.png"
> supersample 4 transparentBackground true pixelSize 0.2
> view zoom_2
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view_Zoom_2_yellow.png"
> supersample 4 transparentBackground true pixelSize 0.2
> view alt
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_view1_no_surface_alt_yellow.png"
> supersample 4 transparentBackground true pixelSize 0.2
> view alt_zoom
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_zoom_alt_yellow.png"
> supersample 4 transparentBackground true pixelSize 0.2
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/Sessions/FigSX_Clash_EJC_ALY_Spliceosome_U5S1_yellow.cxs"
> lighting soft
> lighting flat
> view list
Named views: alt, alt_zoom, view1, zoom, zoom_2
> view alt_zoom
> lighting soft
> select #2/D:84
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> hide #!1 models
> close #1
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/Sessions/FigSX__EJC_ALY_interaction_Details.cxs"
> select zone #2/N:141 5 residues true extend false
Selected 69 atoms
> show sel atoms
> select zone #2/N:141 5 residues true extend true
Selected 80 atoms
> show sel atoms
> select zone #2/N:141,144 5 residues true extend true
Selected 184 atoms
> show sel atoms
> select clear
> select zone #2/N:141,144 5 residues true extend true
Selected 184 atoms
> style sel spheres
Expected a keyword
> style sel sphere
Changed 184 atom styles
> style sel stick
Changed 184 atom styles
> style sel ball
Changed 184 atom styles
> size #2/N:141,144 atomRadius 1.2
Changed 22 atom radii
> size #2/N:141,144 atomRadius 13
Changed 22 atom radii
> size #2/N:141,144 atomRadius 3
Changed 22 atom radii
> size #2/N:141,144 atomRadius 4
Changed 22 atom radii
> size #2/N:141,144 atomRadius 2
Changed 22 atom radii
> size #2/N:141,144 atomRadius 3
Changed 22 atom radii
> size #2/N:141,144 atomRadius 2.5
Changed 22 atom radii
> hide atoms
> select zone #2/N:141,144 5 residues true extend false
Selected 162 atoms
> show sel atoms
> style sel ball
Changed 162 atom styles
> style 2/N:141,144 spheres
Expected a keyword
> size #2/N:141,144 atomRadius 1.2
Changed 22 atom radii
> show 2/N:141,144 a
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> style 2/N:141,144 sphere
Expected a keyword
> size #2/N:141,144 atomRadius 1.2
Changed 22 atom radii
> show #2/N:141,144 atoms
> style #2/N:141,144 sphere
Changed 22 atom styles
> size #2/N:141,144 atomRadius 1.2
Changed 22 atom radii
> hide surfaces
> select clear
> show #2/N surfaces
> transparency #2/n 100
> transparency #2/N 100
> transparency #2/N 95
> transparency #2/N 95ashow #2/A,B s
Missing or invalid "percent" argument: Expected a number
> transparency #2/A,B 95
> close #3
> show #2/A,B surfaces
> transparency #2/A,B 95
> color #2/A #F1D8BC target abcspf
> color #2/C #EB6841 target abcspf
> transparency #2/A,B 95
> graphics silhouettes true width 1 depthJump jump 0.05
Invalid "depthJump" argument: Expected a number
> graphics silhouettes true width 1 depthJump 0.05
> graphics silhouettes true width 1 depthJump 0.01
> color O red target a
> color N blue target a
> undo
> color list all
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
.
> undo
> color O crimson target a
> color N cornflowerblue target a
> hide surfaces
> size #2/N:141,144 atomRadius 1.2
Changed 22 atom radii
> size #2/N:141,144 atomRadius 1.2
Changed 22 atom radii
> size #2/N:141,144 atomRadius 1
Changed 22 atom radii
> size #2/N:141,144 atomRadius 0.8
Changed 22 atom radii
> select zone #2/N:141,144 5 residues true extend false
Selected 162 atoms
> size sel atomRadius 0.5
Changed 162 atom radii
> style sel sphere
Changed 162 atom styles
> size sel atomRadius 0.5
Changed 162 atom radii
> elect zone #2/N:141,144 5 residues true extend false
Unknown command: elect zone #2/N:141,144 5 residues true extend false
> show sel atoms
> style sel ball
Changed 162 atom styles
> size sel atomRadius 0.5
Changed 162 atom radii
> select zone #2/N:141,144 5 residues true extend false
Selected 162 atoms
> show sel atoms
> style sel ball
Changed 162 atom styles
> size sel atomRadius 0.5
Changed 162 atom radii
> size sel atomRadius 1.3
Changed 162 atom radii
> size sel atomRadius 1.5
Changed 162 atom radii
> size sel atomRadius 1.8
Changed 162 atom radii
> select clear
> hbonds #2/N:141 #2/A,B,C
542 hydrogen bonds found
> close #2.9
> hbonds #2/N:141 #2/A,B,C rstrut cross
Expected a keyword
> hbonds #2/N:141 #2/A,B,C restrict cross
20 hydrogen bonds found
> hbonds #2/N:141,144 #2/A,B,C restrict cross
20 hydrogen bonds found
> hbonds #2/N:141,144 #2/A,B,C restrict cross reveeal true
Expected a keyword
> hbonds #2/N:141,144 #2/A,B,C restrict cross reveal true
20 hydrogen bonds found
> hbonds #2/N:141,144 #2/A,B,C restrict cross reveal true distSlop 0.8
31 hydrogen bonds found
> ui mousemode right "tape measure"
> marker segment #1 position 165.6,223.6,200.3 toPosition 165.4,228.6,199.2
> color yellow radius 0.1 label 5.068 labelHeight 0.5068 labelColor yellow
> close #1
> hbonds #2/N:141,144 #2/A,B,C restrict any reveal true distSlop 0.8
673 hydrogen bonds found
> hbonds #2/N:141,144 #2/A,B,C restrict cross reveal true distSlop 0.8
31 hydrogen bonds found
> hbonds #2/N:141,144 #2/A,B,C restrict cross reveal true distSlop 5 saltOnly
> true color yellow dashes 0
30 hydrogen bonds found
> close #2.9-10
> hide atoms
> select zone #2/N:141,144 5 residues true extend false
Selected 162 atoms
> show sel atoms
> style sel ball
Changed 162 atom styles
> size sel atomRadius 0.5
Changed 162 atom radii
> show #2/N:141,144 atoms
> style #2/N:141,144 sphere
Changed 22 atom styles
> size #2/N:141,144 atomRadius 1.2
Changed 22 atom radii
> transparency #2/N 95
> color #2/A #F1D8BC target abcspf
> color #2/C #EB6841 target abcspf
> transparency #2/A,B 95
> color O crimson target a
> color N cornflowerblue target a
> hbonds #2/N:141,144 #2/A,B,C restrict cross reveal true distSlop 0.8
31 hydrogen bonds found
> hbonds #2/N:141,144 #2/A,B,C restrict cross reveal true distSlop 5 saltOnly
> true color yellow dashes 0
30 hydrogen bonds found
> hide #2.9 models
> show #2.9 models
> close #2.9
> select zone #2/N:141,144 5 residues true extend false
Selected 162 atoms
> show sel atoms
> style sel ball
Changed 162 atom styles
> size sel atomRadius 1.5
Changed 162 atom radii
> size sel atomRadius 1.8
Changed 162 atom radii
> size sel atomRadius 2
Changed 162 atom radii
> size sel atomRadius 2.5
Changed 162 atom radii
> size sel atomRadius 2
Changed 162 atom radii
> hbonds #2/N:141,144 #2/A,B,C restrict cross reveal true distSlop 0.8
31 hydrogen bonds found
> hbonds #2/N:141,144 #2/A,B,C restrict cross reveal true distSlop 4 saltOnly
> true color yellow dashes 0
24 hydrogen bonds found
> hbonds #2/N:141,144 #2/A,B,C restrict cross reveal true distSlop 0.8
31 hydrogen bonds found
> select clear
> rename #2.9 id #3
> rename #2.9 hbonds
> hbonds #2/N:141,144 #2/A,B,C restrict cross reveal true distSlop 4 saltOnly
> true color yellow dashes 0
24 hydrogen bonds found
> hide #3 models
> show #3 models
> hbonds #2/N:141,144 #2/A,B,C restrict cross reveal true distSlop 0.8
31 hydrogen bonds found
> hbonds #2/N:141,144 #2/A,B,C restrict cross reveal true distSlop 4 saltOnly
> true color yellow dashes 0 retainCurrent true
24 hydrogen bonds found
> show #2.4 models
> hide #2.4 models
> close #3
> hbonds #2/N:141,144 #2/A,B,C restrict cross reveal true distSlop 0.8
31 hydrogen bonds found
> hbonds #2/N:141,144 #2/A,B,C restrict cross reveal true distSlop 0.8 name
> hbonds
31 hydrogen bonds found
> hbonds #2/N:141,144 #2/A,B,C restrict cross reveal true distSlop 4 saltOnly
> true color yellow dashes 0 name salt
24 hydrogen bonds found
> hide #2.11 models
> show #2.11 models
> hide #2.11 models
> hide #2.9 models
> show #2.11 models
> close #2.11
> close #2.9
> hbonds #2/N:141,144 #2/A,B,C restrict cross reveal true distSlop 6 saltOnly
> true color yellow dashes 0 name salt
33 hydrogen bonds found
> ui mousemode right "tape measure"
> marker segment #1 position 165.4,228.6,199.2 toPosition 165.6,223.6,200.3
> color yellow radius 0.1 label 5.068 labelHeight 0.5068 labelColor yellow
> close #1
> marker segment #1 position 165.4,228.6,199.2 toPosition 165.6,223.6,200.3
> color yellow radius 0.1 label 5.068 labelHeight 0.5068 labelColor yellow
> hide #1.1 models
> marker segment #1 position 169.8,224,189.7 toPosition 167.8,223.7,190.3
> color yellow radius 0.1 label 2.166 labelHeight 0.2166 labelColor yellow
> marker segment #1 position 169.8,224,189.7 toPosition 167,224.8,188.5 color
> yellow radius 0.1 label 3.108 labelHeight 0.3108 labelColor yellow
> close #2.12
> marker segment #1 position 176.8,226,192.7 toPosition 175.5,225.4,195.8
> color yellow radius 0.1 label 3.41 labelHeight 0.341 labelColor yellow
> marker segment #1 position 172.9,227.7,193.6 toPosition 175.5,225.4,195.8
> color yellow radius 0.1 label 4.132 labelHeight 0.4132 labelColor yellow
> ui mousemode right "tape measure"
[Repeated 2 time(s)]
> select #1
10 atoms, 5 bonds, 10 residues, 2 models selected
> hide #!1 models
> ~select #1
Nothing selected
> marker segment #1 position 171.2,222.5,186.8 toPosition 169.8,224,189.7
> color yellow radius 0.1 label 3.58 labelHeight 0.358 labelColor yellow
> marker segment #1 position 171.2,222.5,186.8 toPosition 170.9,224.7,189.5
> color yellow radius 0.1 label 3.555 labelHeight 0.3555 labelColor yellow
> show #!1 models
> close #1.1
> close #1
> marker segment #1 position 167.7,224.7,200.1 toPosition 165.4,228.6,199.2
> color yellow radius 0.1 label 4.602 labelHeight 0.4602 labelColor yellow
> marker segment #1 position 169.8,224,189.7 toPosition 167.8,223.7,190.3
> color yellow radius 0.1 label 2.166 labelHeight 0.2166 labelColor yellow
> marker segment #1 position 167,224.8,188.5 toPosition 170.9,225.9,189 color
> yellow radius 0.1 label 4.046 labelHeight 0.4046 labelColor yellow
> marker delete #1
> marker segment #1 position 176.8,226,192.7 toPosition 176.5,223.7,196.7
> color yellow radius 0.1 label 4.61 labelHeight 0.461 labelColor yellow
> marker segment #1 position 176.6,228.2,193.3 toPosition 175.5,225.4,195.8
> color yellow radius 0.1 label 3.951 labelHeight 0.3951 labelColor yellow
> marker segment #1 position 165.4,228.6,199.2 toPosition 167.5,226.4,200
> color yellow radius 0.1 label 3.121 labelHeight 0.3121 labelColor yellow
> hide #1.1 models
> close #1.1
> close #1
> marker segment #1 position 165.4,228.6,199.2 toPosition 167.7,224.7,200.1
> color yellow radius 0.1 label 4.602 labelHeight 0.4602 labelColor yellow
> marker segment #1 position 176.8,226,192.7 toPosition 176.5,223.7,196.7
> color yellow radius 0.1 label 4.61 labelHeight 0.461 labelColor yellow
> marker segment #1 position 176.6,228.2,193.3 toPosition 175.5,225.4,195.8
> color yellow radius 0.1 label 3.951 labelHeight 0.3951 labelColor yellow
> marker segment #1 position 169.8,224,189.7 toPosition 167.8,223.7,190.3
> color yellow radius 0.1 label 2.166 labelHeight 0.2166 labelColor yellow
> marker segment #1 position 170.9,225.9,189 toPosition 167,224.8,188.5 color
> yellow radius 0.1 label 4.046 labelHeight 0.4046 labelColor yellow
> lifht shadows false
Unknown command: lifht shadows false
> lighting shadows false
> select #2/N:138@CG
1 atom, 1 residue, 1 model selected
> select #2/N:138@NE2
1 atom, 1 residue, 1 model selected
> select up
10 atoms, 10 bonds, 1 residue, 2 models selected
> select #2/B:14@CE
1 atom, 1 residue, 1 model selected
> hide atoms
> how #1/E
Unknown command: how #1/E
> select zone #2/N:141,144 3 residues true extend false
Selected 43 atoms
> show sel atoms
> style sel ball
Changed 43 atom styles
> size sel atomRadius 2
Changed 43 atom radii
> show #2/N:141,144 atoms
> style #2/N:141,144 sphere
Changed 22 atom styles
> size #2/N:141,144 atomRadius 1.2
Changed 22 atom radii
> transparency #2/N 95
> color #2/A #F1D8BC target abcspf
> color #2/C #EB6841 target abcspf
> transparency #2/A,B 95
> color O crimson target a
> color N cornflowerblue target a
> hbonds #2/N:141,144 #2/A,B,C restrict cross reveal true distSlop 0.8 name
> hbonds
31 hydrogen bonds found
> color O crimson target a
> color N cornflowerblue target a
> select zone #2/N:141,144 4 residues true extend false
Selected 98 atoms, 1 surfaces
> show sel atoms
> style sel ball
Changed 98 atom styles
> size sel atomRadius 2
Changed 98 atom radii
> show #2/N:141,144 atoms
> style #2/N:141,144 sphere
Changed 22 atom styles
> size #2/N:141,144 atomRadius 1.2
Changed 22 atom radii
> transparency #2/N 95
> color #2/A #F1D8BC target abcspf
> color #2/C #EB6841 target abcspf
> transparency #2/A,B 95
> color O crimson target a
> color N cornflowerblue target a
> close #1
> how #1/E
Unknown command: how #1/E
> select zone #2/N:141,144 5 residues true extend false
Selected 162 atoms
> show sel atoms
> style sel ball
Changed 162 atom styles
> size sel atomRadius 2
Changed 162 atom radii
> show #2/N:141,144 atoms
> style #2/N:141,144 sphere
Changed 22 atom styles
> size #2/N:141,144 atomRadius 1.2
Changed 22 atom radii
> transparency #2/N 95
> color #2/A #F1D8BC target abcspf
> color #2/C #EB6841 target abcspf
> transparency #2/A,B 95
> color O crimson target a
> color N cornflowerblue target a
> hbonds #2/N:141,144 #2/A,B,C restrict cross reveal true distSlop 0.8 name
> hbonds
31 hydrogen bonds found
> ui mousemode right "tape measure"
> marker segment #1 position 176.8,226,192.7 toPosition 175.5,225.4,195.8
> color yellow radius 0.1 label 3.41 labelHeight 0.341 labelColor yellow
> marker segment #1 position 176.6,228.2,193.3 toPosition 175.5,225.4,195.8
> color yellow radius 0.1 label 3.951 labelHeight 0.3951 labelColor yellow
> marker segment #1 position 167,224.8,188.5 toPosition 170.9,225.9,189 color
> yellow radius 0.1 label 4.046 labelHeight 0.4046 labelColor yellow
> marker segment #1 position 167.8,223.7,190.3 toPosition 169.8,224,189.7
> color yellow radius 0.1 label 2.166 labelHeight 0.2166 labelColor yellow
> marker segment #1 position 165.4,228.6,199.2 toPosition 167.7,224.7,200.1
> color yellow radius 0.1 label 4.602 labelHeight 0.4602 labelColor yellow
> marker segment #1 position 164,230.1,199.9 toPosition 165.6,223.6,200.3
> color yellow radius 0.1 label 6.726 labelHeight 0.6726 labelColor yellow
> hide #1.1 models
> select clear
> select #2/B:83@CG2
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select hide a
Expected an objects specifier or a keyword
> hide sel atoms
> select clear
> ui mousemode right "tape measure"
> marker segment #1 position 172.9,227.7,193.6 toPosition 175.5,225.4,195.8
> color yellow radius 0.1 label 4.132 labelHeight 0.4132 labelColor yellow
> select #2/B:14@CE
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
10 atoms, 10 bonds, 1 residue, 2 models selected
> hide sel atoms
> select #2/N:139@CZ
1 atom, 1 residue, 1 model selected
> select clear
> select #2/N:139@CZ
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 2 models selected
> hide sel atoms
> select clear
> select #2/N:145@CB
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 2 models selected
> hide sel atoms
> select #2/N:146@CG
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> hide sel atoms
> show surfaces
> transprarency 100
Unknown command: transprarency 100
> transparency 100
> transparency 95
> select #2/C:85@CA
1 atom, 1 residue, 1 model selected
> select #2/d:76@OD1
1 atom, 1 residue, 1 model selected
> transparency 90
> ui tool show "Side View"
> select clear
> transparency 50
> transparency q0
Missing or invalid "percent" argument: Expected a number
> transparency 20
> lighting soft intensity 0.2 fillIntensity 0.5 ambientIntensity 1
> lighting soft
> transparency 30
> transparency 34
> color #1/A black target s
> color #2/E black target s
> transparency 35
> transparency 40
> transparency 50
> transparency 40
> transparency 30
> view zoom
> undo
> view name zoom_arg
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX__EJC_ALY_interaction_Details_surface.png"
> transparentBackground true supersample 4 pizelSize 0.05
Expected a keyword
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX__EJC_ALY_interaction_Details_surface.png"
> transparentBackground true supersample 4 pixelSize 0.05
> transparency 100
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX__EJC_ALY_interaction_Details.png"
> transparentBackground true supersample 4 pixelSize 0.05
> ~hbonds
> hide #2.9 models
> hbonds #2/N:141,144 #2/A,B,C restrict cross reveal true distSlop 0.8 name
> hbonds
31 hydrogen bonds found
> show #2.9 models
> hide #2.9 models
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX__EJC_ALY_interaction_Details.png"
> transparentBackground true supersample 4 pixelSize 0.05
> hide surfaces
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX__EJC_ALY_interaction_Details.png"
> transparentBackground true supersample 4 pixelSize 0.05
> show surfaces
> transparency 30
> view name zoom_arg
> view zoom_arg
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX__EJC_ALY_interaction_Details_surface.png"
> transparentBackground true supersample 4 pixelSize 0.05
> hide surfaces
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX__EJC_ALY_interaction_Details.png"
> transparentBackground true supersample 4 pixelSize 0.05
> select #2/N:140@CB
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select sphere
Expected an objects specifier or a keyword
> style sel sphere
Changed 8 atom styles
> style sel atomRadius 1.2
Expected a keyword
> size sel atomRadius 1.2
Changed 8 atom radii
> select clear
> view zoom_arg
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX__EJC_ALY_interaction_Details_surface.png"
> transparentBackground true supersample 4 pixelSize 0.05
> hide surfaces
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX__EJC_ALY_interaction_Details.png"
> transparentBackground true supersample 4 pixelSize 0.05
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/Sessions/FigSX__EJC_ALY_interaction_Details.cxs"
——— End of log from Wed Dec 1 18:26:32 2021 ———
opened ChimeraX session
> show surfaces
> transparency #2 30
> view zoom_arg
> transparency #2/E 50
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX__EJC_ALY_interaction_Details_surface.png"
> transparentBackground true supersample 4 pixelSize 0.05
> transparency #2 50
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX__EJC_ALY_interaction_Details_surface.png"
> transparentBackground true supersample 4 pixelSize 0.05
> hide surfaces
> show surfaces
> hide surfaces
> show surfaces
> size #2/N:141,144,140 atomRadius 0.8
Changed 30 atom radii
> size #2/N:141,144,140 atomRadius 0.5
Changed 30 atom radii
> style #2/N:141,144,140 ball
Changed 30 atom styles
> size #2/N:141,144,140 atomRadius 1.2
Changed 30 atom radii
> size #2/N:141,144,140 atomRadius 2
Changed 30 atom radii
> view lsit
Expected an objects specifier or a view name or a keyword
> view list
Named views: alt, alt_zoom, view1, zoom, zoom_2, zoom_arg
> view zoom_arg
> hide surfaces
> ui tool show "Side View"
> show surfaces
> hide surfaces
> select #2/N:144
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #2/N:139
23 atoms, 22 bonds, 2 residues, 2 models selected
> select up
80 atoms, 81 bonds, 10 residues, 2 models selected
> show sel atoms
> show surfaces
> hide surfaces
> lighting gentle
> hide #!1 models
> show #!1 models
> select #2/B:116
7 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/B:76
15 atoms, 14 bonds, 2 residues, 2 models selected
> transaprency #2/B:76-117 50 target c
Unknown command: transaprency #2/B:76-117 50 target c
> transparency #2/B:76-117 50 target c
> transparency #2/B:76-117 70 target c
> close #1
> ui mousemode right "tape measure"
> marker segment #1 position 175.5,225.4,195.8 toPosition 176.6,228.2,193.3
> color yellow radius 0.1 label 3.951 labelHeight 0.3951 labelColor yellow
> marker segment #1 position 167.7,224.7,200.1 toPosition 165.4,228.6,199.2
> color yellow radius 0.1 label 4.602 labelHeight 0.4602 labelColor yellow
> marker segment #1 position 169.8,224,189.7 toPosition 167.8,223.7,190.3
> color yellow radius 0.1 label 2.166 labelHeight 0.2166 labelColor yellow
> marker segment #1 position 175.5,225.4,195.8 toPosition 172.9,227.7,193.6
> color yellow radius 0.1 label 4.132 labelHeight 0.4132 labelColor yellow
> lighting soft
> lighting soft intensity 0.2 fillIntensity 0.5 ambientIntensity 1
> lighting soft intensity 0.5 fillIntensity 0.5 ambientIntensity 1
> lighting soft intensity 0.1 fillIntensity 0.5 ambientIntensity 1
> lighting soft intensity 0.1 fillIntensity 0.8 ambientIntensity 1
> lighting soft intensity 0.1 fillIntensity 0.8 ambientIntensity 2
> lighting soft intensity 0.1 fillIntensity 0.8 ambientIntensity 1
> lighting soft intensity 0.1 fillIntensity 1 ambientIntensity 1
> lighting soft intensity 0.1 fillIntensity 0.8 ambientIntensity 1
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> select zone #2/N:141,144 5 residues true extend false
Selected 169 atoms, 1 surfaces
> show sel atoms
> style sel ball
Changed 169 atom styles
> size sel atomRadius 1
Changed 169 atom radii
> close #1
> size sel atomRadius 1.5
Changed 162 atom radii
> size sel atomRadius 1.2
Changed 162 atom radii
> size sel atomRadius 1.3
Changed 162 atom radii
> style #2/N:141,144,140 ball
Changed 30 atom styles
> size #2/N:141,144,140 atomRadius 1.3
Changed 30 atom radii
> select clear
> select /B:83@CB
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select /B:14
9 atoms, 8 bonds, 1 residue, 1 model selected
> undo
[Repeated 1 time(s)]
> select clear
> select /B:83@CG2
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
103 atoms, 107 bonds, 13 residues, 2 models selected
> select down
7 atoms, 6 bonds, 1 residue, 2 models selected
> hide sel atoms
Drag select of 1 residues
> select clear
> select /N:146@CG
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> hide sel atoms
> select /N:138@ND1
1 atom, 1 residue, 1 model selected
> select up
10 atoms, 10 bonds, 1 residue, 2 models selected
> hide sel atoms
> ui mousemode right "tape measure"
> marker segment #1 position 175.5,225.4,195.8 toPosition 176.8,226,192.7
> color yellow radius 0.1 label 3.41 labelHeight 0.341 labelColor yellow
> marker segment #1 position 175.5,225.4,195.8 toPosition 172.9,227.7,193.6
> color yellow radius 0.1 label 4.132 labelHeight 0.4132 labelColor yellow
> marker segment #1 position 167.7,224.7,200.1 toPosition 165.4,228.6,199.2
> color yellow radius 0.1 label 4.602 labelHeight 0.4602 labelColor yellow
> hbonds #2/N:141,144 #2/A,B,C restrict cross reveal true distSlop 0.8 name
> hbonds
31 hydrogen bonds found
> show #2.9 models
> select clear
> addh
Summary of feedback from adding hydrogens to
refine_run4_real_space_refined_noSS.pdb #2
---
warnings | Not adding hydrogens to refine_run4_real_space_refined_noSS.pdb
#2/D LYS 164 CB because it is missing heavy-atom bond partners
Not adding hydrogens to refine_run4_real_space_refined_noSS.pdb #2/I LYS 164
CB because it is missing heavy-atom bond partners
Not adding hydrogens to refine_run4_real_space_refined_noSS.pdb #2/N LYS 164
CB because it is missing heavy-atom bond partners
Not adding hydrogens to refine_run4_real_space_refined_noSS.pdb #2/d LYS 164
CB because it is missing heavy-atom bond partners
Not adding hydrogens to refine_run4_real_space_refined_noSS.pdb #2/i LYS 164
CB because it is missing heavy-atom bond partners
1 messages similar to the above omitted
notes | No usable SEQRES records for refine_run4_real_space_refined_noSS.pdb
(#2) chain A; guessing termini instead
No usable SEQRES records for refine_run4_real_space_refined_noSS.pdb (#2)
chain B; guessing termini instead
No usable SEQRES records for refine_run4_real_space_refined_noSS.pdb (#2)
chain C; guessing termini instead
No usable SEQRES records for refine_run4_real_space_refined_noSS.pdb (#2)
chain D; guessing termini instead
No usable SEQRES records for refine_run4_real_space_refined_noSS.pdb (#2)
chain E; guessing termini instead
25 messages similar to the above omitted
Chain-initial residues that are actual N termini:
refine_run4_real_space_refined_noSS.pdb #2/A MET 23,
refine_run4_real_space_refined_noSS.pdb #2/B SER 3,
refine_run4_real_space_refined_noSS.pdb #2/C GLY 65,
refine_run4_real_space_refined_noSS.pdb #2/D LEU 74,
refine_run4_real_space_refined_noSS.pdb #2/F MET 23,
refine_run4_real_space_refined_noSS.pdb #2/G SER 3,
refine_run4_real_space_refined_noSS.pdb #2/H GLY 65,
refine_run4_real_space_refined_noSS.pdb #2/I LEU 74,
refine_run4_real_space_refined_noSS.pdb #2/K MET 23,
refine_run4_real_space_refined_noSS.pdb #2/L SER 3,
refine_run4_real_space_refined_noSS.pdb #2/M GLY 65,
refine_run4_real_space_refined_noSS.pdb #2/N LEU 74,
refine_run4_real_space_refined_noSS.pdb #2/a MET 23,
refine_run4_real_space_refined_noSS.pdb #2/b SER 3,
refine_run4_real_space_refined_noSS.pdb #2/c GLY 65,
refine_run4_real_space_refined_noSS.pdb #2/d LEU 74,
refine_run4_real_space_refined_noSS.pdb #2/f MET 23,
refine_run4_real_space_refined_noSS.pdb #2/g SER 3,
refine_run4_real_space_refined_noSS.pdb #2/h GLY 65,
refine_run4_real_space_refined_noSS.pdb #2/i LEU 74,
refine_run4_real_space_refined_noSS.pdb #2/k MET 23,
refine_run4_real_space_refined_noSS.pdb #2/l SER 3,
refine_run4_real_space_refined_noSS.pdb #2/m GLY 65,
refine_run4_real_space_refined_noSS.pdb #2/n LEU 74
Chain-initial residues that are not actual N termini:
refine_run4_real_space_refined_noSS.pdb #2/D THR 104,
refine_run4_real_space_refined_noSS.pdb #2/I THR 104,
refine_run4_real_space_refined_noSS.pdb #2/N THR 104,
refine_run4_real_space_refined_noSS.pdb #2/d THR 104,
refine_run4_real_space_refined_noSS.pdb #2/i THR 104,
refine_run4_real_space_refined_noSS.pdb #2/n THR 104
Chain-final residues that are actual C termini:
refine_run4_real_space_refined_noSS.pdb #2/B ILE 146,
refine_run4_real_space_refined_noSS.pdb #2/G ILE 146,
refine_run4_real_space_refined_noSS.pdb #2/L ILE 146,
refine_run4_real_space_refined_noSS.pdb #2/b ILE 146,
refine_run4_real_space_refined_noSS.pdb #2/g ILE 146,
refine_run4_real_space_refined_noSS.pdb #2/l ILE 146
Chain-final residues that are not actual C termini:
refine_run4_real_space_refined_noSS.pdb #2/A PRO 404,
refine_run4_real_space_refined_noSS.pdb #2/C PRO 155,
refine_run4_real_space_refined_noSS.pdb #2/D THR 182,
refine_run4_real_space_refined_noSS.pdb #2/D ASP 84,
refine_run4_real_space_refined_noSS.pdb #2/F PRO 404,
refine_run4_real_space_refined_noSS.pdb #2/H PRO 155,
refine_run4_real_space_refined_noSS.pdb #2/I THR 182,
refine_run4_real_space_refined_noSS.pdb #2/I ASP 84,
refine_run4_real_space_refined_noSS.pdb #2/K PRO 404,
refine_run4_real_space_refined_noSS.pdb #2/M PRO 155,
refine_run4_real_space_refined_noSS.pdb #2/N THR 182,
refine_run4_real_space_refined_noSS.pdb #2/N ASP 84,
refine_run4_real_space_refined_noSS.pdb #2/a PRO 404,
refine_run4_real_space_refined_noSS.pdb #2/c PRO 155,
refine_run4_real_space_refined_noSS.pdb #2/d THR 182,
refine_run4_real_space_refined_noSS.pdb #2/d ASP 84,
refine_run4_real_space_refined_noSS.pdb #2/f PRO 404,
refine_run4_real_space_refined_noSS.pdb #2/h PRO 155,
refine_run4_real_space_refined_noSS.pdb #2/i THR 182,
refine_run4_real_space_refined_noSS.pdb #2/i ASP 84,
refine_run4_real_space_refined_noSS.pdb #2/k PRO 404,
refine_run4_real_space_refined_noSS.pdb #2/m PRO 155,
refine_run4_real_space_refined_noSS.pdb #2/n THR 182,
refine_run4_real_space_refined_noSS.pdb #2/n ASP 84
3556 hydrogen bonds
Adding 'H' to refine_run4_real_space_refined_noSS.pdb #2/D THR 104
Adding 'H' to refine_run4_real_space_refined_noSS.pdb #2/I THR 104
Adding 'H' to refine_run4_real_space_refined_noSS.pdb #2/N THR 104
Adding 'H' to refine_run4_real_space_refined_noSS.pdb #2/d THR 104
Adding 'H' to refine_run4_real_space_refined_noSS.pdb #2/i THR 104
1 messages similar to the above omitted
refine_run4_real_space_refined_noSS.pdb #2/A PRO 404 is not terminus, removing
H atom from 'C'
refine_run4_real_space_refined_noSS.pdb #2/C PRO 155 is not terminus, removing
H atom from 'C'
refine_run4_real_space_refined_noSS.pdb #2/D THR 182 is not terminus, removing
H atom from 'C'
refine_run4_real_space_refined_noSS.pdb #2/F PRO 404 is not terminus, removing
H atom from 'C'
refine_run4_real_space_refined_noSS.pdb #2/H PRO 155 is not terminus, removing
H atom from 'C'
13 messages similar to the above omitted
34518 hydrogens added
> hbonds #2/N:141,144 #2/A,B,C restrict cross reveal true distSlop 0.8 name
> hbonds
28 hydrogen bonds found
> hide h
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hbonds #2/N:141,144 #2/A,B,C restrict cross reveal false distSlop 0.8 name
> hbonds
28 hydrogen bonds found
> hide H
> hbonds #2/N:141,144 #2/A,B,C restrict cross reveal false distSlop 0.8 name
> hbonds
28 hydrogen bonds found
> hbonds #2/N:141,144 #2/A,B,C restrict cross reveal true distSlop 0.8 name
> hbonds
28 hydrogen bonds found
> hide H
> hbonds #2/N:141,144 #2/A,B,C restrict cross reveal false distSlop 1 name
> hbonds
33 hydrogen bonds found
> hide #2.9 models
> show #2.9 models
> hbonds #2/N:141-144 #2/A,B,C restrict any reveal false distSlop 1 name
> hbonds
656 hydrogen bonds found
> hbonds #2/N:141-144 #2/A,B,C restrict any reveal false distSlop 1 name
> hbonds intraMol flase
Invalid "intraMol" argument: Expected true or false (or 1 or 0)
> hbonds #2/N:141-144 #2/A,B,C restrict any reveal false distSlop 1 name
> hbonds intraMol false
86 hydrogen bonds found
> hbonds #2/N: #2/A,B,C restrict any reveal false distSlop 1 name hbonds
> intramol false
Expected a keyword
> hbonds #2/N #2/A,B,C restrict any reveal false distSlop 1 name hbonds
> intraMol false
91 hydrogen bonds found
> hbonds #2/N #2/A,B,C restrict any reveal true distSlop 1 name hbonds
> intraMol false
91 hydrogen bonds found
> close #2.9
> hide H
> hide #2/A,B,C atoms
> select zone #2/N:140,141,144 5 residues true extend false
Selected 448 atoms
> show sel atoms
> style sel ball
Changed 448 atom styles
> size sel atomRadius 1.3
Changed 448 atom radii
> hide #!1 models
> close #1
> hide H
> delete H
> select clear
> select /N:138@CE1
1 atom, 1 residue, 1 model selected
> select /N:138@CE1
1 atom, 1 residue, 1 model selected
> select up
10 atoms, 10 bonds, 1 residue, 2 models selected
> hide sek
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide sel atoms
> select /N:139@CE1
1 atom, 1 residue, 1 model selected
> select clear
> select /N:146@CG
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> hide sel atoms
> select /B:17
11 atoms, 11 bonds, 1 residue, 1 model selected
> show surfaces
> select clear
> hide #2/E surfaces
> hide #2/A,B,C surfaces
> show #2/A,B,C surfaces
> hide surfaces
> ui mousemode right "tape measure"
> marker segment #1 position 165.6,223.6,200.3 toPosition 165.4,228.6,199.2
> color yellow radius 0.1 label 5.068 labelHeight 0.5068 labelColor yellow
> marker segment #1 position 172.8,230,193.7 toPosition 172.5,231.9,195.2
> color yellow radius 0.1 label 2.467 labelHeight 0.2467 labelColor yellow
> close #1
> marker segment #1 position 172.8,230,193.7 toPosition 171.5,231.4,198.8
> color yellow radius 0.1 label 5.406 labelHeight 0.5406 labelColor yellow
> marker segment #1 position 167.7,224.7,200.1 toPosition 165.4,228.6,199.2
> color yellow radius 0.1 label 4.602 labelHeight 0.4602 labelColor yellow
> view name arg_zoom_v2
> marker segment #1 position 175.5,225.4,195.8 toPosition 176.8,226,192.7
> color yellow radius 0.1 label 3.41 labelHeight 0.341 labelColor yellow
> close #1
> marker segment #1 position 175.5,225.4,195.8 toPosition 176.8,226,192.7
> color yellow radius 0.1 label 3.41 labelHeight 0.341 labelColor yellow
> marker segment #1 position 175.5,225.4,195.8 toPosition 172.9,227.7,193.6
> color yellow radius 0.1 label 4.132 labelHeight 0.4132 labelColor yellow
> marker segment #1 position 167.7,224.7,200.1 toPosition 165.4,228.6,199.2
> color yellow radius 0.1 label 4.602 labelHeight 0.4602 labelColor yellow
> marker segment #1 position 167.8,223.7,190.3 toPosition 169.8,224,189.7
> color yellow radius 0.1 label 2.166 labelHeight 0.2166 labelColor yellow
> marker segment #1 position 167,224.8,188.5 toPosition 170.9,225.9,189 color
> yellow radius 0.1 label 4.046 labelHeight 0.4046 labelColor yellow
> view arg_zoom_v2
> hide #1.1 models
> select #2/B:13@CD2
1 atom, 1 residue, 1 model selected
> select up
10 atoms, 10 bonds, 1 residue, 2 models selected
> select up
100 atoms, 104 bonds, 11 residues, 2 models selected
> select clear
> select #2/B:17@CE1
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 2 models selected
> hide sel atoms
> select #2/B:14@CD
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> hide sel atoms
> select clear
> select #2/A:384@OD2
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> hide sel atoms
> select #2/B:103@CB
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> hide sel atoms
> select #2/B:83
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
103 atoms, 107 bonds, 13 residues, 2 models selected
> select clear
> select #2/B:83@CB
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> hide sel atoms
> select #2/A:356@OD1
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> hide sel atoms
> select #2/A:355
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:285@CG
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> select #2/A:388@CG1
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> hide sel atoms
> select #2/A:355@CB
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/A:358@CZ
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> hide sel atoms
> select clear
> select #2/B:20@OE1
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> hide sel atoms
> select clear
> select #2/A:354@CD1
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> hide sel atoms
> select clear
> select #2/N:115@CD2
1 atom, 1 residue, 1 model selected
> select #2/N:115@CZ
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 2 models selected
> hide sel atoms
Drag select of 7 atoms, 5 residues, 7 bonds
> select clear
[Repeated 1 time(s)]
> view list
Named views: alt, alt_zoom, arg_zoom_v2, view1, zoom, zoom_2, zoom_arg
> view zoom_arg
> select #2/B:21
11 atoms, 11 bonds, 1 residue, 1 model selected
> select clear
> select #2/N:142@CB
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 2 models selected
> hide sel atoms
> select clear
> view name arg_zoom_v3
> show surfaces
> lighting gentle
> graphics silhouettes true width 1 depthJump 0.01
> graphics silhouettes true width 1 depthJump 0.1
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/Sessions/FigSX__EJC_ALY_interaction_Details_v2.cxs"
> view list
Named views: alt, alt_zoom, arg_zoom_v2, arg_zoom_v3, view1, zoom, zoom_2,
zoom_arg
> view arg_zoom_v3
[Repeated 1 time(s)]
> show surfaces
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX__EJC_ALY_interaction_Details_surface_v3.png"
> transparentBackground true supersample 4 pixelSize 0.05
> hide surfaces
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX__EJC_ALY_interaction_Details_details_v3.png"
> transparentBackground true supersample 4 pixelSize 0.05
> turn y 180
> ~clip
> hide #!1 models
> transaprency #2/B:76-117 0 target c
Unknown command: transaprency #2/B:76-117 0 target c
> transparency #2/B:76-117 0 target c
> transparency #2/B 0 target c
> select #2/N:139@CZ
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 2 models selected
> hide sel
> select clear
> select #2/B:16@NZ
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> hide sel
> select clear
Drag select of 19 atoms, 17 bonds
> select up
20 atoms, 17 bonds, 4 residues, 4 models selected
> select up
36 atoms, 34 bonds, 4 residues, 4 models selected
> select clear
Drag select of 19 atoms, 16 bonds
> select up
36 atoms, 34 bonds, 4 residues, 4 models selected
> hide sel
> select clear
> select #2/N:161@CE
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 2 models selected
> hide sel atoms
Drag select of 5 atoms, 5 bonds
> hide sel atoms
> select #2/K:206@CA
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> select #2/N:81@OD1
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> hide sel atoms
> hide #4/d cartoons
> hide #2/d cartoons
> select #2/N:145@OG
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 2 models selected
> hide sel atoms
> show surfaces
> select clear
> hide surfaces
> show surfaces /2/A,B,C,N
Expected ',' or a keyword
> show #2/A,B,C,N surfaces
> hode #2/A,B,C,N s
Unknown command: hode #2/A,B,C,N s
> hide #2/A,B,C,N surfaces
> size #2/N:144 atomRadius 2
Changed 11 atom radii
> size #2/N:144 atomRadius 4
Changed 11 atom radii
> size #2/N:144 atomRadius 5
Changed 11 atom radii
> size #2/N:144 atomRadius 3
Changed 11 atom radii
> size #2/N:144 atomRadius 4
Changed 11 atom radii
> size #2/N:144 stickRadius 4
Changed 10 bond radii
> size #2/N:144 stickRadius 1
Changed 10 bond radii
> size #2/N:144 atomRadius 4
Changed 11 atom radii
> view name view5
> view view5
> show surfaces
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX__EJC_ALY_interaction_Details_surface_view5.png"
> transparentBackground true supersample 4 pixelSize 0.05
> hide surfaces
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX__EJC_ALY_interaction_Details_details_view5.png"
> transparentBackground true supersample 4 pixelSize 0.05
> show surfaces #2/A,B,C,N
Expected ',' or a keyword
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX__EJC_ALY_interaction_Details_surface_view5.png"
> transparentBackground true supersample 4 pixelSize 0.05
> show #2/A,B,C,N surfaces
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX__EJC_ALY_interaction_Details_surface_view5.png"
> transparentBackground true supersample 4 pixelSize 0.05
> hide #2/N surfaces
> show #2/N surfaces
> view list
Named views: alt, alt_zoom, arg_zoom_v2, arg_zoom_v3, view1, view5, zoom,
zoom_2, zoom_arg
> view zoom
> view view5
> hide surfaces
> show #!1 models
> size #2/N:144 atomRadius 2
Changed 11 atom radii
> size #2/N:144stickRadius 1
Expected a keyword
> size #2/N:144stickRadius 0.5
Expected a keyword
> size #2/N:144 stickRadius 0.5
Changed 10 bond radii
> view name view5_zoomed
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX__EJC_ALY_interaction_Details_details_view5_zoomed.png"
> transparentBackground true supersample 4 pixelSize 0.05
> show #1.1 models
> hide #1.1 models
> lighting gentle
> lighting soft
> lighting full
> lighting gentle
> lighting soft intensity 0.1 fillIntensity 1 ambientIntensity 1
> lighting soft intensity 0.1 fillIntensity 0.9 ambientIntensity 1
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX__EJC_ALY_interaction_Details_details_view5_zoomed.png"
> transparentBackground true supersample 4 pixelSize 0.05
> color #1 black transparency 0
> color #1 #ebebeb transparency 0
> color #1 #929292 transparency 0
> color #1 #ff2600 transparency 0
> color #1 black transparency 0
> hide #!1 models
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX__EJC_ALY_interaction_Details_details_view5_zoomed.png"
> transparentBackground true supersample 4 pixelSize 0.05
> show #!1 models
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX__EJC_ALY_interaction_Details_details_view5_zoomed.png"
> transparentBackground true supersample 4 pixelSize 0.05
> hide #!1 models
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX__EJC_ALY_interaction_Details_details_view5_zoomed.png"
> transparentBackground true supersample 4 pixelSize 0.05
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/Sessions/FigSX__EJC_ALY_interaction_Details_v2.cxs"
——— End of log from Thu Dec 2 11:17:26 2021 ———
opened ChimeraX session
> view list
Named views: alt, alt_zoom, arg_zoom_v2, arg_zoom_v3, view1, view5,
view5_zoomed, zoom, zoom_2, zoom_arg
> view view5
> lighting gentle
> show #2/A,B,C,N surfaces
> transparency
Missing or invalid "percent" argument: Expected a number
> transparency 30
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX__EJC_ALY_interaction_Details_surface_view5_tr30.png"
> transparentBackground true supersample 4 pixelSize 0.05
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/Sessions/FigSX__EJC_ALY_interaction_Details_v2.cxs"
——— End of log from Thu Dec 2 11:47:48 2021 ———
opened ChimeraX session
> windowsize 800 800
> view list
Named views: alt, alt_zoom, arg_zoom_v2, arg_zoom_v3, view1, view5,
view5_zoomed, zoom, zoom_2, zoom_arg
> color #1/A #F1D8BC target abcspf
> color #1/B #EAA439 target abcspf
> color #1/C #EB6841 target abcspf
> color #1/A #F1D8BC target abcspf
> color #1/B #EB6841EAA439 target abcspf
> color #1/C #EAA439 target abcspf
> color #2/A #F1D8BC target abcspf
> color #2/B #EAA439 target abcspf
> color #2/C #EB6841 target abcspf
> color O crimson target a
> color N cornflowerblue target a
> view view5
> show #2/A,B,C,N surfaces
> transaprency 30
Unknown command: transaprency 30
> view view5
> show #2/A,B,C,N surfaces
> transparency 30
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX__EJC_ALY_interaction_Details_surface_view5_tr30.png"
> transparentBackground true supersample 4 pixelSize 0.05
> hide surfaces
> size #2/N:144 stickRadius 0.5
Changed 10 bond radii
> size #2/N:144 atomRadius 2
Changed 11 atom radii
> view view5_zoomed
> show #1
> lighting soft intensity 0.1 fillIntensity 0.8 ambientIntensity 1
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/FigSX__EJC_ALY_interaction_Details_details_view5_zoomed.png"
> transparentBackground true supersample 4 pixelSize 0.05
> save "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/chimerax/Sessions/FigSX__EJC_ALY_interaction_Details_v2.cxs"
——— End of log from Thu Dec 2 14:18:13 2021 ———
opened ChimeraX session
> open "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/pdbs/eIF4A3_closed.pdb"
Summary of feedback from opening /Users/matthias.vorlaender/Documents/OneDrive
- VBC/figures_shared/figures/pdbs/eIF4A3_closed.pdb
---
warnings | Start residue of secondary structure not found: HELIX 23 23 LYS B
54 SER B 67 1 14
Start residue of secondary structure not found: HELIX 24 24 ILE B 69 LYS B 71
1 3
Start residue of secondary structure not found: HELIX 25 25 LEU B 107 ASN B
111 1 5
Start residue of secondary structure not found: HELIX 26 26 PRO B 116 PHE B
141 1 26
Start residue of secondary structure not found: HELIX 27 27 GLU C 86 PHE C 93
1 8
313 messages similar to the above omitted
Cannot find LINK/SSBOND residue MG (702 )
Cannot find LINK/SSBOND residue MG (702 )
Cannot find LINK/SSBOND residue MG (702 )
Cannot find LINK/SSBOND residue MG (702 )
Cannot find LINK/SSBOND residue MG (702 )
Chain information for eIF4A3_closed.pdb #3
---
Chain | Description
A | No description available
> open "/Users/matthias.vorlaender/Documents/OneDrive -
> VBC/figures_shared/figures/pdbs/eIFA3_apo_pdb_2hxy_monomer.pdb"
Summary of feedback from opening /Users/matthias.vorlaender/Documents/OneDrive
- VBC/figures_shared/figures/pdbs/eIFA3_apo_pdb_2hxy_monomer.pdb
---
warnings | Start residue of secondary structure not found: HELIX 17 17 PHE B
40 GLY B 44 1 5
Start residue of secondary structure not found: HELIX 18 18 ARG B 46 GLY B 57
1 12
Start residue of secondary structure not found: HELIX 19 19 SER B 62 GLY B 75
1 14
Start residue of secondary structure not found: HELIX 20 20 THR B 89 CYS B 99
1 11
Start residue of secondary structure not found: HELIX 21 21 THR B 115 GLY B
130 1 16
90 messages similar to the above omitted
Chain information for eIFA3_apo_pdb_2hxy_monomer.pdb #4
---
Chain | Description
A | No description available
> hide #!2 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> hide #!3 models
> show #4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> view
> mmaker #4 to #3
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 eIF4A3_closed.pdb, chain A (#3) with
eIFA3_apo_pdb_2hxy_monomer.pdb, chain A (#4), sequence alignment score =
1768.6
RMSD between 132 pruned atom pairs is 0.880 angstroms; (across all 367 pairs:
24.231)
> show #!3 models
> view
> show #!2 models
> show #2 cartoons
> hide #!2 models
> hide #4 models
> show #!2 models
> mmaker #3 to #2/A bring #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 refine_run4_real_space_refined_noSS.pdb, chain A (#2) with
eIF4A3_closed.pdb, chain A (#3), sequence alignment score = 1958.3
RMSD between 382 pruned atom pairs is 0.000 angstroms; (across all 382 pairs:
0.000)
> show #4 models
> color #3/4 A,a,F,f,K,k #F1D8BC target abcspf
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color #3/4 #F1D8BC target abcspf
> color #3,4 #F1D8BC target abcspf
> hide #!2 models
> morph
Missing or invalid "structures" argument: empty atom specifier
> morph #4,3
Computed 51 frame morph #5
> coordset #5 1,51
> close #5
> morph #4,3 frames 70
Computed 71 frame morph #5
> coordset #5 1,71
> show #!2 models
> hide #!2 models
> morph #4,3 frames 50 rate ramp down
Invalid "rate" argument: 'ramp' is ambiguous, could be ramp down, ramp up
> morph #4,3 frames 50 rate rampdown
Invalid "rate" argument: Should be one of 'linear', 'ramp down', 'ramp up', or
'sinusoidal'
> morph #4,3 frames 70 rate ramp down
Invalid "rate" argument: 'ramp' is ambiguous, could be ramp down, ramp up
> morph #4,3 frames 70 rate ramp Down
Invalid "rate" argument: 'ramp' is ambiguous, could be ramp down, ramp up
> morph #4,3 frames 70 rate rampDown
Invalid "rate" argument: Should be one of 'linear', 'ramp down', 'ramp up', or
'sinusoidal'
> morph #4,3 frames 70 ramp down
Expected a keyword
> morph #4,3 frames 70 rate ramp up
Invalid "rate" argument: 'ramp' is ambiguous, could be ramp down, ramp up
> morph #4,3 frames 70 rate sinusoidal
Computed 71 frame morph #6
> coordset #6 1,71
> morph #4,3 rate ramp up
Invalid "rate" argument: 'ramp' is ambiguous, could be ramp down, ramp up
> morph #4,3 rate ramp down
Invalid "rate" argument: 'ramp' is ambiguous, could be ramp down, ramp up
OpenGL version: 4.1 INTEL-14.7.8
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,2
Processor Name: Quad-Core Intel Core i7
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 512 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
Boot ROM Version: 1715.40.15.0.0 (iBridge: 19.16.10549.0.0,0)
Software:
System Software Overview:
System Version: macOS 10.15.7 (19H2)
Kernel Version: Darwin 19.6.0
Time since boot: 10 days 14:32
Graphics/Displays:
Intel Iris Plus Graphics:
Chipset Model: Intel Iris Plus Graphics
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x8a53
Revision ID: 0x0007
Metal: Supported, feature set macOS GPUFamily2 v1
Displays:
HP Z32:
Resolution: 6016 x 3384
UI Looks like: 3008 x 1692 @ 60 Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: CN401619VF
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
Connection Type: Thunderbolt/DisplayPort
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: 2021.5.30
cftime: 1.5.1.1
charset-normalizer: 2.0.7
ChimeraX-AddCharge: 1.1.5
ChimeraX-AddH: 2.1.10
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: 1.30.2
ChimeraX-AtomicLibrary: 4.1.5
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
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-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: 1.3rc202111110135
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.1
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-ItemsInspection: 1.0
ChimeraX-Label: 1.1
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
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
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
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.5.0
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
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: 2.7.3
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.0
ParmEd: 3.2.0
parso: 0.8.2
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.22
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: 1.11.2
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: 2.1.0
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
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
Change History (4)
comment:1 by , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Structure Comparison |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → morph rate/ramp syntax |
comment:3 by , 4 years ago
| Resolution: | → not a bug |
|---|---|
| Status: | assigned → closed |
Yes, you just need to put "ramp up" in quotation marks. Any option value that has spaces (with the possible exception of a color name) should have quotation marks around it.
The general command usage page mentions this issue:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html>
Still I agree maybe should strive to have option values that aren't multiple words, or that can be disambiguated on the first word.
follow-up: 4 comment:4 by , 4 years ago
Great, thanks!
On 04.12.21, 01:46, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:
#5728: morph rate/ramp syntax
--------------------------------------------+-------------------------
Reporter: matthias.vorlaender@… | Owner: Tom Goddard
Type: defect | Status: closed
Priority: normal | Milestone:
Component: Structure Comparison | Version:
Resolution: not a bug | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
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Changes (by Elaine Meng):
* status: assigned => closed
* resolution: => not a bug
Comment:
Yes, you just need to put "ramp up" in quotation marks. Any option value
that has spaces (with the possible exception of a color name) should have
quotation marks around it.
The general command usage page mentions this issue:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html>
Still I agree maybe should strive to have option values that aren't
multiple words, or that can be disambiguated on the first word.
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5728#comment:3>
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