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Opened 4 years ago
Last modified 4 years ago
#4566 assigned enhancement
Cap colors not matching
| Reported by: | Tristan Croll | Owned by: | Tom Goddard |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Surface | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19041
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
When molecular surfaces are coloured using "color fromAtoms sel target s", the clip cap colors don't match (still the original surface colors?). Turning clip caps off and on again doesn't help.
Log:
UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:/Users/tic20/OneDrive - University of
> Cambridge/Figures/overview.cxs"
Log from Wed Apr 21 17:17:49 2021UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:/Users/tic20/Dropbox (Cambridge
> University)/Structures/Pu_Qian/RCLH1LH2/Figures/overview.cxs"
Log from Wed Apr 21 15:14:25 2021UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:/Users/tic20/Dropbox (Cambridge
> University)/Structures/Pu_Qian/RCLH1LH2/Figures/overview.cxs"
Log from Thu Apr 15 18:32:59 2021UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open overview.cxs
Log from Wed Apr 14 18:27:11 2021
> alias preview_toolshed toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu; toolshed reload available
> alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu;
> toolshed reload available
> alias st isolde step $*
> alias aw isolde add water $*
> alias awsf isolde add water sim false
> alias al isolde add ligand $*
> alias so setattr sel atoms occupancy $*
UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open model_1b_working_noh_real_space_refined.cif
Summary of feedback from opening model_1b_working_noh_real_space_refined.cif
---
warnings | Skipping chem_comp category: Missing column 'type' near line 979
Missing entity information. Treating each chain as a separate entity.
Missing second residue in struct_conn "C00001"
Missing second residue in struct_conn "C00002"
Missing second residue in struct_conn "C00003"
Missing second residue in struct_conn "C00004"
Missing second residue in struct_conn "C00005"
20 messages similar to the above omitted
Missing first residue in struct_conn "C00026"
Missing second residue in struct_conn "C00027"
Missing first residue in struct_conn "C00028"
Missing first residue in struct_conn "C00029"
Missing second residue in struct_conn "C00030"
Missing second residue in struct_conn "C00031"
Missing second residue in struct_conn "C00032"
Missing first residue in struct_conn "C00033"
Missing second residue in struct_conn "C00034"
Missing second residue in struct_conn "C00035"
Missing second residue in struct_conn "C00036"
Missing second residue in struct_conn "C00037"
Missing second residue in struct_conn "C00038"
2 messages similar to the above omitted
Missing first residue in struct_conn "C00041"
Missing first residue in struct_conn "C00042"
Missing first residue in struct_conn "C00043"
Missing first residue in struct_conn "C00044"
Missing second residue in struct_conn "C00045"
Missing first residue in struct_conn "C00046"
Missing first residue in struct_conn "C00047"
Missing second residue in struct_conn "C00048"
Missing first residue in struct_conn "C00049"
Missing first residue in struct_conn "C00050"
Missing first residue in struct_conn "C00051"
Missing first residue in struct_conn "C00052"
Missing first residue in struct_conn "C00053"
18 messages similar to the above omitted
Missing second residue in struct_conn "C00072"
Missing second residue in struct_conn "C00073"
Missing second residue in struct_conn "C00074"
Missing second residue in struct_conn "C00075"
Missing second residue in struct_conn "C00076"
23 messages similar to the above omitted
Missing first residue in struct_conn "C00100"
Missing second residue in struct_conn "C00101"
Missing second residue in struct_conn "C00102"
Missing first residue in struct_conn "C00103"
Missing first residue in struct_conn "C00104"
Missing first residue in struct_conn "C00105"
Missing first residue in struct_conn "C00106"
Missing first residue in struct_conn "C00107"
1 messages similar to the above omitted
Invalid residue range for struct_conf "1": invalid entity "AA", near line 601
Invalid residue range for struct_conf "2": invalid entity "AA", near line 602
Invalid residue range for struct_conf "3": invalid entity "AA", near line 603
Invalid residue range for struct_conf "4": invalid entity "AB", near line 604
Invalid residue range for struct_conf "5": invalid entity "AB", near line 605
226 messages similar to the above omitted
Atom C1 is not in the residue template for GPC /AA:1007
Atom C1 is not in the residue template for GPC /AB:1005
Atom C1 is not in the residue template for GPC /AC:1005
Atom C1 is not in the residue template for GPC /AD:1007
Atom C1 is not in the residue template for GPC /AE:1007
19 messages similar to the above omitted
Atom C26 is not in the residue template for PEX /H1:1005
Atom C1 is not in the residue template for LMY /L:1019
Atom C26 is not in the residue template for PEX /M:1007
Atom C1 is not in the residue template for GPC /aa:1003
Atom C1 is not in the residue template for GPC /ab:1003
Atom C1 is not in the residue template for GPC /ac:1003
Atom C1 is not in the residue template for GPC /ad:1003
Atom C1 is not in the residue template for GPC /ae:1003
1 messages similar to the above omitted
Atom C26 is not in the residue template for PEX /af:1001
Atom C1 is not in the residue template for LMY /ag:1005
Atom C1 is not in the residue template for GPC /ag:1007
Atom C1 is not in the residue template for GPC /ah:1003
Atom C1 is not in the residue template for GPC /ai:1005
Atom C1 is not in the residue template for LMZ /ai:1001
7 messages similar to the above omitted
Atom C26 is not in the residue template for PEX /ba:1001
Atom C26 is not in the residue template for PEX /bb:1003
Atom C26 is not in the residue template for PEX /bc:1003
Atom C26 is not in the residue template for PEX /bd:1003
Atom C26 is not in the residue template for PEX /be:1003
12 messages similar to the above omitted
Atom C2A is not in the residue template for GUX /CG:2
Atom C2A is not in the residue template for GUX /MG:2
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Skipping chem_comp category: Missing column 'type' near line 57678
Skipping chem_comp category: Missing column 'type' near line 58583
Skipping chem_comp category: Missing column 'type' near line 58981
Skipping chem_comp category: Missing column 'type' near line 59543
Skipping chem_comp category: Missing column 'type' near line 60102
13 messages similar to the above omitted
Chain information for model_1b_working_noh_real_space_refined.cif #1
---
Chain | Description
AA AB AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | No
description available
AC AD | No description available
BA BC BF BG BH BJ BK BL BM BN BO BP BU BX ba bb bc bd be bf bg bh bi bj bk bl
bm bo bp | No description available
BB BD BE BI BQ BR BS BT BV BW bn | No description available
C | No description available
C1 | No description available
C2 | No description available
H1 | No description available
H2 | No description available
L | No description available
M | No description available
aa | No description available
ab ad ae af ag ah ai aj al am an ao | No description available
ac | No description available
ak ap | No description available
> open
> /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2021_01_final_maps/model1b/class4a_r_2.47A_postprocess_masked.mrc
Opened class4a_r_2.47A_postprocess_masked.mrc, grid size 400,400,400, pixel
0.999, shown at level 0.0175, step 2, values float32
> volume #2 step 1
> surface dust #2
> volume #2 color #bf404000
> volume #2 color #ffffff10
> set bgColor white
> volume #2 color #bfb1b1
> volume #2 color #756d6d
> volume #2 color #757474
> volume #2 color #c4c1c1
> volume #2 color #c4c4c4
> volume #2 color #c8c8c8
> volume #2 color #252525
> volume #2 color #222222
> volume #2 color #1e1e1e
> volume #2 color #191919
> volume #2 color #171616
> volume #2 color #141414
> volume #2 color #171616
> volume #2 color #333131
> volume #2 color #333333
> volume #2 color #3a3a3a
> volume #2 color #404040
> volume #2 color #424242
> volume #2 color #4242425d
> volume #2 color #42424266
> volume #2 color #42424269
> volume #2 color #4242426a
> volume #2 color #4242427e
> volume #2 color #4242428c
> volume #2 color #4242428a
> volume #2 color #42424260
> volume #2 color #42424246
> volume #2 color #4242423e
> volume #2 color #4242423d
> volume #2 color #42424235
> volume #2 color #42424234
> volume #2 color #42424233
> volume #2 color #42424230
> volume #2 color #4242422f
> volume #2 color #4242422e
> volume #2 color #4242422c
> volume #2 color #42424223
> volume #2 color #42424221
> volume #2 color #42404021
> volume #2 color #e2dcdc21
> volume #2 color #e2e1e121
> volume #2 color #f7f6f621
> volume #2 color #f7f7f721
> volume #2 color #ffffff21
> volume #2 color #f4f4f421
> volume #2 color #f1f1f121
> volume #2 color #e1e1e121
> volume #2 color #cacaca21
> volume #2 color #b7b7b721
> volume #2 color #98989821
> volume #2 color #8e8e8e21
> volume #2 color #85858521
> volume #2 color #84848421
> volume #2 color #83838321
> volume #2 color #80808021
> volume #2 color #7a7a7a21
> volume #2 color #74747421
> volume #2 color #71717121
> volume #2 color #78787821
> volume #2 color #90909021
> volume #2 color #aaaaaa21
> volume #2 color #b0b0b021
> cartoon
> hide
> dssp
> select /C
2616 atoms, 2576 bonds, 16 pseudobonds, 422 residues, 2 models selected
> color /C green
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> color /C lime
> color /M magenta
> color /L orange
> select /H1
721 atoms, 718 bonds, 84 residues, 1 model selected
> color /H1 cyan
> color /H2 lightseagreen
> select /S
Nothing selected
> color /C1 red
> color /C2 olivegreen
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color /C2 olive
> select /a*
9878 atoms, 10044 bonds, 64 pseudobonds, 1093 residues, 2 models selected
> volume #2 level 0.03183
> volume #2 level 0.03737
> color sel yellow
> color sel gold
> color sel yellow
> color /A* gold
> color /b*,B* cornflowerblue
> select clear
> select :GPC
1800 atoms, 1760 bonds, 40 residues, 1 model selected
> show
> hide protein
> hide
> select :GPC
1800 atoms, 1760 bonds, 40 residues, 1 model selected
> show sel
> color sel orangered
> select clear
> select :BCL
7128 atoms, 7560 bonds, 432 pseudobonds, 108 residues, 2 models selected
> show sel
> color sel blue
> select clear
> select :HEA,HEM,HEC
172 atoms, 184 bonds, 16 pseudobonds, 4 residues, 2 models selected
> show sel
> color sel pink
> select clear
> volume #2 color #eeeeec
> color zone #2 near #1&(protein|:BCL,HEM,HEC,GPC)
> select clear
> hide #!1 models
> color zone #2 near #1&(protein|:BCL,HEM,HEC,GPC,MAN,RAM,GUX,NDG)
> hide #!2 models
> show #!1 models
> show :MAN,RAM,GUX,NDG
> color /C,CG lime
> color /M,MG magenta
> select :HEA,HEM,HEC
172 atoms, 184 bonds, 16 pseudobonds, 4 residues, 2 models selected
> color sel pink
> select clear
> show #!2 models
> color zone #2 near #1&(protein|:BCL,HEM,HEC,GPC,MAN,RAM,GUX,NDG)
> select clear
> hide #!1 models
> select #1&~(protein|:BCL,HEM,HEC,GPC,MAN,RAM,GUX,NDG)
6671 atoms, 6374 bonds, 566 residues, 1 model selected
> color sel white
> color zone #2 near #1&(protein|:BCL,HEM,HEC,GPC,MAN,RAM,GUX,NDG)
> open
> /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2021_01_final_maps/model1b/class4a_r_2.47A_postprocess_masked.mrc
Opened class4a_r_2.47A_postprocess_masked.mrc, grid size 400,400,400, pixel
0.999, shown at level 0.0175, step 2, values float32
> volume #3 step 1
> volume #3 color #b0b0b021
> surface dust #3
> volume #3 level 0.01753
> volume #3 level 0.02399
> volume #3 level 0.01338
> volume #3 level 0.01707
> select clear
> volume #3 level 0.02122
> volume #3 level 0.01661
> volume #2 level 0.02952
> volume #3 level 0.01799
> surface dust #3
> volume gaussian #3 bfactor 80
> volume #4 color #b0b0b021
> volume #4 level 0.01281
> select clear
> volume #2 level 0.02574
> show #!1 models
> volume #2 level 0.02
> volume #2 level 0.03
> hide #!1 models
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> save overview.cxs
opened ChimeraX session
> hide #!4 models
> hide #!2 models
> show #!1 models
> show :CD4
> select :PEX
900 atoms, 880 bonds, 20 residues, 1 model selected
> select ~protein
15877 atoms, 15984 bonds, 448 pseudobonds, 726 residues, 8 models selected
> ui tool show Shell
/opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
UserWarning: IPython History requires SQLite, your history will not be saved
warn("IPython History requires SQLite, your history will not be saved")
> select /bi:21
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select :PGW
51 atoms, 50 bonds, 1 residue, 1 model selected
> show sel
> select :LMY
116 atoms, 118 bonds, 2 residues, 1 model selected
> show sel
> select :LMZ
55 atoms, 55 bonds, 1 residue, 1 model selected
> show sel
> select :CD4
504 atoms, 498 bonds, 6 residues, 1 model selected
> color sel green
> style sel sphere
Changed 504 atom styles
> select clear
> select /H1:1003@C05
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 1 bond, 4 residues, 1 model selected
> select clear
> select :PGW
51 atoms, 50 bonds, 1 residue, 1 model selected
> color sel tan
> style sel sphere
Changed 51 atom styles
> select clear
> select up
6 atoms, 3 bonds, 3 residues, 1 model selected
> select up
171 atoms, 173 bonds, 3 residues, 1 model selected
> color sel orange
> style sel sphere
Changed 171 atom styles
> select clear
> select :CDL
Nothing selected
> select :CD4
504 atoms, 498 bonds, 6 residues, 1 model selected
> select clear
> select :CD4,PGW,LMY,LMZ
726 atoms, 721 bonds, 10 residues, 1 model selected
> hide ~sel
> select clear
> cofr centerOfView showPivot true
> dssp
> ~cartoon /M
> cartoon /M
> select clear
> roll x 90
> roll x 90 1
> stop
> roll x 90 1
> ui mousemode right "mark point"
> marker #5 position 196.7,203,208.7 color yellow radius 1
> ui mousemode right "resize markers"
> marker change #5:1 radius 56.26
> ui mousemode right "move markers"
> marker change #5:1 position 199.8,200.8,208.8
> transparency sel 60
> transparency sel 60 target a
> marker change #5:1 position 200.3,200.9,208.8
> marker change #5:1 position 199.6,200.1,208.8
> ui mousemode right "resize markers"
> marker change #5:1 radius 56.26
> marker change #5:1 radius 57.4
> select clear
> ui mousemode right "move markers"
> marker change #5:1 position 199.8,199.4,208.8
> ui mousemode right "delete markers"
> show #!2 models
> show #!4 models
> hide #!1 models
> select clear
> color /M plum target s
> color /M plum
> color zone #2 near #1
> color /M,MG plum
> color zone #2 near #1
> volume #4 level 0.015
> volume #4 level 0.0145
> save overview.cxs
> close #3
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> hide #!2 models
> show #!1 models
> color /C greenyellow
> color /C lightgreeen
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color /C limegreen
> color /C lime
> color /C limegreen
> color /C,CG limegreen
> show #!2 models
> color zone #2 near #1
> color /C,CG lime
> color zone #2 near #1
> hide #!2 models
> color #2 white
> color zone #2 near #1&(protein|/CG,MG)
> show #!2 models
> select clear
> hide #!1 models
> color /A*&protein goldenrod
> color zone #2 near #1&(protein|/CG,MG)
> color /A*&protein khaki
> color zone #2 near #1&(protein|/CG,MG)
> hide #!2 models
> show #!1 models
> hide #!4 models
> show #!4 models
> show #!2 models
> open colour_scheme.cxs
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 275, in execute
cmd.run(cmd_text)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 100, in cmd_open
return Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 154, in provider_open
name or model_name_from_path(fi.file_name)), provider_kw)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 390, in collated_open
return func(*func_args, **func_kw)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 925, in open
session.restore(stream, path=path, resize_window=resize_window)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 608, in restore
version = serialize.pickle_deserialize(stream)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/serialize.py", line 57, in pickle_deserialize
return unpickler.load()
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/serialize.py", line 51, in find_class
raise pickle.UnpicklingError("global '%s' is forbidden" % fullname)
_pickle.UnpicklingError: global 'olor #1 white.color /a*&protein yellow' is
forbidden
_pickle.UnpicklingError: global 'olor #1 white.color /a*&protein yellow' is
forbidden
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/serialize.py", line 51, in find_class
raise pickle.UnpicklingError("global '%s' is forbidden" % fullname)
See log for complete Python traceback.
> open colour_scheme.cxc
> color #1 white
> color /a*&protein yellow
> color /A*&protein khaki
> color /b*,B*&protein cornflowerblue
> color /C1&protein red
> color /C&protein lime
> color /CG lime
> color /M&protein plum
> color /MG plum
> color /C&protein green
> color /L&protein orange
> color /H1&protein cyan
> color /H2&protein lightseagreen
> color /C2&protein olive
> color :BCL blue
> color :GPC orangered
> color :HEC pink
> color zone #2 near #1
executed colour_scheme.cxc
> open colour_scheme.cxc
> color #1 white
> color /a*&protein yellow
> color /A*&protein khaki
> color /b*,B*&protein cornflowerblue
> color /C1&protein red
> color /C&protein lime
> color /CG lime
> color /M&protein plum
> color /MG plum
> color /L&protein orange
> color /H1&protein cyan
> color /H2&protein lightseagreen
> color /C2&protein olive
> color :BCL blue
> color :GPC orangered
> color :HEC pink
> color zone #2 near #1
executed colour_scheme.cxc
> hide
> select clear
> select clear
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> open colour_scheme.cxc
> color #1 white
> color /a*&protein yellow
> color /A*&protein khaki
> color /b*,B*&protein cornflowerblue
> color /C1&protein red
> color /C&protein palegreen
> color /CG palegreen
> color /M&protein plum
> color /MG plum
> color /L&protein orange
> color /H1&protein cyan
> color /H2&protein lightseagreen
> color /C2&protein olive
> color :BCL blue
> color :GPC orangered
> color :HEC pink
> color zone #2 near #1
executed colour_scheme.cxc
> open colour_scheme.cxc
> color #1 white
> color /a*&protein yellow
> color /A*&protein khaki
> color /b*,B*&protein cornflowerblue
> color /C1&protein red
> color /C&protein palegreen
> color /CG palegreen
> color /M&protein plum
> color /MG plum
> color /L&protein orange
> color /H1&protein cyan
> color /H2&protein mediumseagreen
> color /C2&protein olive
> color :BCL blue
> color :GPC orangered
> color :HEC pink
> color zone #2 near #1
executed colour_scheme.cxc
> open colour_scheme.cxc
> color #1 white
> color /a*&protein yellow
> color /A*&protein khaki
> color /b*,B*&protein cornflowerblue
> color /C1&protein red
> color /C&protein palegreen
> color /CG palegreen
> color /M&protein plum
> color /MG plum
> color /L&protein orange
> color /H1&protein cyan
> color /H2&protein lightseagreen
> color /C2&protein olive
> color :BCL blue
> color :GPC orangered
> color :HEC pink
> color zone #2 near #1
executed colour_scheme.cxc
> open colour_scheme.cxc
> color #1 white
> color /a*&protein yellow
> color /A*&protein khaki
> color /b*,B*&protein cornflowerblue
> color /C1&protein red
> color /C&protein palegreen
> color /CG palegreen
> color /M&protein plum
> color /MG plum
> color /L&protein orange
> color /H1&protein cyan
> color /H2&protein lightseagreen
> color /C2&protein mediumseagreen
> color :BCL blue
> color :GPC orangered
> color :HEC pink
> color zone #2 near #1
executed colour_scheme.cxc
> open colour_scheme.cxc
> color #1 white
> color /a*&protein yellow
> color /A*&protein khaki
> color /b*,B*&protein cornflowerblue
> color /C1&protein red
> color /C&protein palegreen
> color /CG palegreen
> color /M&protein plum
> color /MG plum
> color /L&protein orange
> color /H1&protein cyan
> color /H2&protein lightseagreen
> color /C2&protein orangered
> color :BCL blue
> color :GPC orangered
> color :HEC pink
> color zone #2 near #1
executed colour_scheme.cxc
> volume #2 level 0.027
> open colour_scheme.cxc
> color #1 white
> color /a*&protein yellow
> color /A*&protein khaki
> color /b*,B*&protein cornflowerblue
> color /C1&protein red
> color /C&protein palegreen
> color /CG palegreen
> color /M&protein plum
> color /MG plum
> color /L&protein orange
> color /H1&protein cyan
> color /H2&protein lightseagreen
> color /C2&protein orangered
> color :BCL blue
> color :GPC orangered
> color :HEC pink
> color zone #2 near #1
executed colour_scheme.cxc
> usage color zone
color zone surfaces near an atoms specifier [distance a number] [sharpEdges
true or false] [bondPointSpacing a number] [farColor a color] [update true or
false]
— color surfaces to match nearby atoms
> open colour_scheme.cxc
> color #1 white
> color /a*&protein yellow
> color /A*&protein khaki
> color /b*,B*&protein cornflowerblue
> color /C1&protein red
> color /C&protein palegreen
> color /CG palegreen
> color /M&protein plum
> color /MG plum
> color /L&protein orange
> color /H1&protein cyan
> color /H2&protein lightseagreen
> color /C2&protein orangered
> color :BCL blue
> color :GPC orangered
> color :HEC pink
> color zone #2 near #1 distance 2.5
executed colour_scheme.cxc
> lighting soft
> ui tool show Shell
> open colour_scheme.cxc
> color #1 white
> color /a*&protein yellow
> color /A*&protein khaki
> color /b*,B*&protein cornflowerblue
> color /C1&protein red
> color /C&protein palegreen
> color /CG palegreen
> color /M&protein plum
> color /MG plum
> color /L&protein orange
> color /H1&protein cyan
> color /H2&protein lightseagreen
> color /C2&protein orangered
> color :BCL blue
> color :GPC purple
> color :HEC pink
> color zone #2 near #1 distance 2.5
executed colour_scheme.cxc
> usage view
view [objects [frames]] [clip true or false] [cofr true or false] [orient]
[pad a number]
— adjust camera so everything is visible
objects: an objects specifier or a view name
frames: an integer ≥ 1
Subcommands are:
* view delete
* view initial
* view list
* view matrix
* view name
* view position
> view matrix
camera position:
0.8585,0.51231,0.022873,210.59,-0.51145,0.85209,0.11121,269.01,0.037483,-0.10717,0.99354,789.33
model positions:
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0
> usage view matrix
view matrix [camera a position] [models model positions] [coordinateSystem a
coordinate-system]
— set camera and model positions
> open colour_scheme.cxc
> color #1 white
> color /a*&protein yellow
> color /A*&protein khaki
> color /b*,B*&protein cornflowerblue
> color /C1&protein red
> color /C&protein palegreen
> color /CG palegreen
> color /M&protein plum
> color /MG plum
> color /L&protein orange
> color /H1&protein cyan
> color /H2&protein lightseagreen
> color /C2&protein orangered
> color :BCL blue
> color :GPC purple
> color :HEC pink
> color zone #2 near #1 distance 2.5
executed colour_scheme.cxc
> open colour_scheme.cxc
> color #1 white
> color /a*&protein yellow
> color /A*&protein khaki
> color /b*,B*&protein cornflowerblue
> color /C1&protein red
> color /C&protein palegreen
> color /CG palegreen
> color /M&protein plum
> color /MG plum
> color /L&protein orange
> color /H1&protein cyan
> color /H2&protein lightseagreen
> color /C2&protein orangered
> color :BCL blue
> color :GPC purple
> color :HEC pink
> color zone #2 near #1 distance 2.5
executed colour_scheme.cxc
> open colour_scheme.cxc
> color #1 white
> color /a*&protein yellow
> color /A*&protein khaki
> color /b*,B*&protein cornflowerblue
> color /C1&protein red
> color /C&protein palegreen
> color /CG palegreen
> color /M&protein plum
> color /MG plum
> color /L&protein orange
> color /H1&protein cyan
> color /H2&protein lightseagreen
> color /C2&protein orangered
> color :BCL blue
> color :GPC purple
> color :HEC pink
> color zone #2 near #1 distance 2.5
> view matrix camera
> 0.8585,0.51231,0.022873,210.59,-0.51145,0.85209,0.11121,269.01,0.037483,-0.10717,0.99354,789.33
executed colour_scheme.cxc
> save overview.cxs
> hide #!1 models
> graphics silhouettes true
> save overview_top.png supersample 5
> graphics silhouettes false
> save overview_top.png supersample 5
> save overview_top_transp.png supersample 5 transparentBackground true
> roll x 90 1
Drag select of 2 class4a_r_2.47A_postprocess_masked.mrc , 4
class4a_r_2.47A_postprocess_masked.mrc gaussian
> select clear
> roll x -90 1
> roll x -90 1
> camera ortho
> roll x 90 1
> save overview_top.png supersample 5
> roll x -90 1
Drag select of 2 class4a_r_2.47A_postprocess_masked.mrc , 4
class4a_r_2.47A_postprocess_masked.mrc gaussian
> select clear
Drag select of 2 class4a_r_2.47A_postprocess_masked.mrc , 4
class4a_r_2.47A_postprocess_masked.mrc gaussian
> select clear
> roll x 90 1
> roll x -90 1
Drag select of 2 class4a_r_2.47A_postprocess_masked.mrc , 4
class4a_r_2.47A_postprocess_masked.mrc gaussian
> select clear
> roll x 90 1
> view matrix
camera position:
0.84541,0.53405,-0.0088516,192.17,-0.53366,0.84525,0.02768,220.5,0.022263,-0.018676,0.99958,792.84
model positions:
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0
> save overview_top.png supersample 5
> usage lighting
lighting [preset] [direction direction] [intensity a number] [color a color]
[fillDirection fillDirection] [fillIntensity a number] [fillColor a color]
[ambientIntensity a number] [ambientColor a color] [depthCue true or false]
[depthCueStart a number] [depthCueEnd a number] [depthCueColor a color]
[moveWithCamera true or false] [shadows true or false] [qualityOfShadows a
text string] [depthBias a number] [multiShadow an integer] [msMapSize an
integer] [msDepthBias a number]
— report or alter lighting parameters
preset: one of default, flat, full, gentle, simple, or soft
direction: some numbers
fillDirection: some numbers
lighting model models [depthCue true or false] [shadows true or false]
[multiShadow true or false] [directional true or false]
— Turn off depth cue or shadows for individual models even when globally they
are enabled.
> lighting ambientIntensity
Missing "ambientIntensity" keyword's argument
> lighting ambientIntensity 1
> lighting ambientIntensity 2
> lighting ambientIntensity 1.5
> lighting ambientIntensity 1.7
> lighting ambientIntensity 1.4
> lighting soft
> lighting fillIntensity 1
> lighting fillIntensity 0.6
> lighting fillIntensity 0.5
> lighting fillIntensity 0.4
> lighting fillIntensity 0.3
> lighting soft
> lighting fillIntensity 0.2
> lighting fillIntensity 0.25
> lighting fillIntensity 0.15
> lighting soft
> lighting fillIntensity 0.1
> lighting fillIntensity 0.15
> lighting fillIntensity 0.15 ambient 1.2
Expected keyword "ambientColor" or "ambientIntensity"
> lighting fillIntensity 0.15 ambientIntensity 1.2
> lighting fillIntensity 0.15 ambientIntensity 1.4
> lighting fillIntensity 0.15 ambientIntensity 1.6
> lighting soft fillIntensity 0.2
> lighting soft
> lighting soft fillIntensity 0.2
> lighting soft
> lighting soft fillIntensity 0.2
> lighting soft fillIntensity 0.25
> lighting soft fillIntensity 0.3
> lighting soft fillIntensity 0.5
> lighting soft fillIntensity 0.2
> save overview.cxs
> save overview_top.png supersample 5
> roll x -90 1
> save overview_side.png supersample 5
> roll x -90 1
> save overview_bottom.png supersample 5
> roll x 180 1
> show #!1 models
> hide #!2 models
> hide #!4 models
> lighting soft
> lighting soft fillIntensity 0.05
> usage lighting
lighting [preset] [direction direction] [intensity a number] [color a color]
[fillDirection fillDirection] [fillIntensity a number] [fillColor a color]
[ambientIntensity a number] [ambientColor a color] [depthCue true or false]
[depthCueStart a number] [depthCueEnd a number] [depthCueColor a color]
[moveWithCamera true or false] [shadows true or false] [qualityOfShadows a
text string] [depthBias a number] [multiShadow an integer] [msMapSize an
integer] [msDepthBias a number]
— report or alter lighting parameters
preset: one of default, flat, full, gentle, simple, or soft
direction: some numbers
fillDirection: some numbers
lighting model models [depthCue true or false] [shadows true or false]
[multiShadow true or false] [directional true or false]
— Turn off depth cue or shadows for individual models even when globally they
are enabled.
> lighting soft fillIntensity 0.05 ambient 1
Expected keyword "ambientColor" or "ambientIntensity"
> lighting soft fillIntensity 0.05 ambientIntensity 1
> lighting soft fillIntensity 0.05 ambientIntensity 1.2
> lighting soft fillIntensity 0.05 ambientIntensity 1.4
> lighting soft
> lighting full
> lighting soft
> show ~protein
> hide H
> hide :LMT
> hide :LMY,CD4,LMZ
> show :LMY,CD4,LMZ
> style stick
Changed 56476 atom styles
> select clear
> save overview_top_cartoon.png supersample 5
> roll x -90 1
> save overview_side_cartoon.png supersample 5
> roll x -90 1
> save overview_bottom_cartoon.png supersample 5
> show
> hide protein
> select clear
> hide #!1 models
> show #!2 models
> show #!4 models
> roll x -90 1
> roll x -90 1
> usage save session
Expected fewer arguments
> usage save
save name [format format] [format-specific arguments]
— save data to various file formats
name: name of a file to save/write; a name of 'browse' will bring up a file
browser
format: one of aln, bmp image, brix, clustal, cmap, dcd, fasta, gif image,
gltf, imagic, jpeg image, markers, mmcif, mol2, mrc, mtz, obj, pdb, pir, png
image, positions, ppm image, pseudobonds, segger, session, stl, tiff image,
vtk, x3d, or xyz
format-specific arguments: format-specific arguments; to see their syntax use
the 'usage save format format' command, where format is as per the above
> usage save format session
save name [includeMaps true or false] [uncompressed true or false] [version an
integer]
— save data to session format
names: name of a file to save/write; a name of 'browse' will bring up a file
browser
> save overview.cxs includeMaps true
opened ChimeraX session
> show #!1 models
> hide #!2 models
> hide #!4 models
> select /CG,MG
106 atoms, 106 bonds, 8 residues, 1 model selected
> color sel byhetero
> hide :HOH
> select /M:331
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel
> select /M:331@OG
1 atom, 1 residue, 1 model selected
> select /MG:1@C1
1 atom, 1 residue, 1 model selected
> select /MG:1@O4
1 atom, 1 residue, 1 model selected
> select /MG:1@O2
1 atom, 1 residue, 1 model selected
> select /MG:2@C1
1 atom, 1 residue, 1 model selected
> select /MG:2@O4
1 atom, 1 residue, 1 model selected
> select /MG:3@C1
1 atom, 1 residue, 1 model selected
> select /CG
53 atoms, 53 bonds, 4 residues, 1 model selected
> select /C:108
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
135 atoms, 138 bonds, 18 residues, 1 model selected
> select down
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel
> color sel byhetero
> select /C:108@OG1
1 atom, 1 residue, 1 model selected
> select /CG:1@O4
1 atom, 1 residue, 1 model selected
> select /CG:2@C1
1 atom, 1 residue, 1 model selected
> select /CG:3@C1
1 atom, 1 residue, 1 model selected
> usage camera ortho
camera [type] [fieldOfView a number] [eyeSeparation a number]
[pixelEyeSeparation a number] [cubePixels an integer]
— adjust camera parameters
type: one of 360, 360sbs, 360tb, dome, mono, ortho, sbs, stereo, or tb
> open "C:/Users/tic20/Dropbox (Cambridge
> University)/Structures/Pu_Qian/RCLH1LH2/Figures/initial_view.cxc"
> cartoon #1
> show #1:BCL,GPC,HEC
> transparency #1 0 target ar
> hide #1 models
> show #2,4 models
> volume #2 level 0.035
> volume #4 level 0.0145
> color #4 70,70,70,13
> color #1 white
> color /aa-ap&protein gold
> color /AA-AX&protein khaki
> color /ba-bp,BA-BX&protein cornflowerblue
> color /C1&protein red
> color /C&protein palegreen
> color /CG palegreen
> color /M&protein plum
> color /MG plum
> color /L&protein orange
> color /H1&protein cyan
> color /H2&protein lightseagreen
> color /C2&protein orangered
> color :BCL blue
> color :GPC purple
> color :HEC pink
> color zone #2 near #1 distance 2.5
> view matrix camera
> 0.84541,0.53405,-0.0088516,192.17,-0.53366,0.84525,0.02768,220.5,0.022263,-0.018676,0.99958,792.84
> lighting soft fillIntensity 0.2
> camera ortho
> cofr showPivot false
> graphics silhouettes false
executed initial_view.cxc
> camera fieldOfView 100
> usage camera
camera [type] [fieldOfView a number] [eyeSeparation a number]
[pixelEyeSeparation a number] [cubePixels an integer]
— adjust camera parameters
type: one of 360, 360sbs, 360tb, dome, mono, ortho, sbs, stereo, or tb
> camera fieldOfView 200
> save overview.cxs includeMaps true
opened ChimeraX session
> open "C:/Users/tic20/Dropbox (Cambridge
> University)/Structures/Pu_Qian/RCLH1LH2/Figures/initial_view.cxc"
> cartoon #1
> show #1:BCL,GPC,HEC
> cartoon style thickness 1
> transparency #1 0 target ar
> hide #1 models
> show #2,4 models
> volume #2 level 0.035
> volume #4 level 0.0145
> color #4 70,70,70,13
> color #1 white
> color /aa-ap&protein gold
> color /AA-AX&protein khaki
> color /ba-bp,BA-BX&protein cornflowerblue
> color /C1&protein red
> color /C&protein palegreen
> color /CG palegreen
> color /M&protein plum
> color /MG plum
> color /L&protein orange
> color /H1&protein cyan
> color /H2&protein lightseagreen
> color /C2&protein orangered
> color :BCL blue
> color :GPC purple
> color :HEC pink
> color zone #2 near #1 distance 2.5
> view matrix camera
> 0.84541,0.53405,-0.0088516,192.17,-0.53366,0.84525,0.02768,220.5,0.022263,-0.018676,0.99958,792.84
> lighting soft fillIntensity 0.2
> camera ortho
> cofr showPivot false
> graphics silhouettes false
executed initial_view.cxc
> open "C:/Users/tic20/Dropbox (Cambridge
> University)/Structures/Pu_Qian/RCLH1LH2/Figures/Overview/overview_images.cxc"
> cartoon #1
> hide #1
> show #1:BCL,GPC,MAN,RAM,GUX,NDG
> save overview_top.png supersample 5 height 2000
> hide #2,4 models
> show #1 models
> save overview_top_cartoon.png supersample 5 height 2000
> show #2,4 models
> hide #1 models
> roll x -90 1
> save overview_side.png supersample 5 height 2000
> hide #2,4 models
> show #1 models
> save overview_side_cartoon.png supersample 5 height 2000
> show #2,4 models
> hide #1 models
> roll x -90 1
> save overview_bottom.png supersample 5 height 2000
> hide #2,4 models
> show #1 models
> save overview_bottom_cartoon.png supersample 5 height 2000
> show #2,4 models
> hide #1 models
executed overview_images.cxc
> roll y -90 1
> roll y 90 1
> roll x -90 1
> roll x -90 1
> roll x -90 1
> roll x -90 1
> roll x -90 1
> roll x -90 1
> save "C:/Users/tic20/Dropbox (Cambridge
> University)/Structures/Pu_Qian/RCLH1LH2/Figures/overview.cxs"
opened ChimeraX session
> open "C:/Users/tic20/OneDrive - University of
> Cambridge/Figures/initial_view.cxc"
> alias savefig save $1 supersample 5 height 2000
> name B800
> #1/AA:1003|/AB:1003|/AC:1003|/AD:1003|/AE:1005|/AF:1005|/AG:1005|/AH:1007|/AI:1007|/AJ:1007|/AK:1007|/AL:1007|/AM:1007|/AN:1007|/AO:1005|/AP:1007|/AQ:1007|/AR:1005|/AS:1007|/AT:1007|/AU:1007|/AV:1003|/AW:1005|/AX:1007
> name B816
> #1/AA:1001|/AB:1001|/AC:1001|/AD:1001|/AE:1001|/AF:1001|/AG:1003|/AH:1003|/AI:1003|/AJ:1003|/AK:1003|/AL:1003|/AM:1003|/AN:1003|/AO:1003|/AP:1003|/AQ:1003|/AR:1003|/AS:1003|/AT:1003|/AU:1003|/AV:1009|/AW:1003|/AX:1003|/BA:1001|/BB:1001|/BC:1001|/BD:1003|/BE:1001|/BF:1001|/BG:1001|/BH:1001|/BI:1001|/BJ:1001|/BK:1001|/BL:1001|/BM:1001|/BN:1001|/BO:1001|/BP:1001|/BQ:1001|/BR:1001|/BS:1005|/BT:1001|/BU:1001|/BV:1001|/BW:1001|/BX:1005
> name B868 #1/aa-ap,ba-bp:BCL
> cartoon #1
> show #1:BCL,GPC,HEC
> cartoon style thickness 1
> transparency #1 0 target ar
> hide #1 models
> show #2,4 models
> volume #2 level 0.035
> volume #4 level 0.0145
> color #4 70,70,70,13
> color #1 whitesmoke
> color #1/aa-ap&protein gold
> color #1/AA-AX&protein khaki
> color #1/ba-bp,BA-BX&protein cornflowerblue
> color #1/C1&protein red
> color #1/C&protein palegreen
> color #1/CG palegreen
> color #1/M&protein plum
> color #1/MG plum
> color #1/L&protein orange
> color #1/H1&protein cyan
> color #1/H2&protein lightseagreen
> color #1/C2&protein mediumvioletred
> color #1:BCL blue
> color #1:GPC orangered
> color #1:CRT gold
> color #1:HEC pink
> color #1:MQ8 lime
> color zone #2 near #1 distance 2.5
> view matrix camera
> 0.68819,0.72554,-0.0017072,196.22,-0.72415,0.68701,0.06017,239.38,0.044827,-0.040171,0.99819,792.04
> zoom pixelSize 0.262
> cofr pivot 196.5,204.73,205.79
> lighting soft fillIntensity 0.2 depthCue true
> camera ortho
> cofr showPivot false
> graphics silhouettes false color black
executed initial_view.cxc
> open "C:/Users/tic20/OneDrive - University of
> Cambridge/Figures/Figure_4/all_chromophores_and_quinones.cxc"
> lighting full depthCue false
> graphics silhouettes true color grey
> ~cartoon #1
> show #1 models
> hide #2,4 models
> hide
> color B800 hotpink
> color B816 limegreen
> color B868 royalblue
> color :FE orange
> color :MQ8 lime
> color :BPH orange
> color :CRT gold
> color /L:1001|/M:1005 red
> color /L:1003|/M:1003 blue
> setattr :HEC bonds radius 0.5
Assigning radius attribute to 184 items
> setattr ~:HEC bonds radius 0.25
Assigning radius attribute to 57836 items
> style @FE,MG sphere
Changed 113 atom styles
> show B800|B816|B868|:GPC,CRT,Fe,HEC,MQ8,BPH,BCL
> view matrix camera
> 0.72553,-0.59683,0.34262,402.85,0.68702,0.65722,-0.30997,18.517,-0.040173,0.46027,0.88687,723.18
> zoom pixelSize 0.212
> cartoon /BA-BX&helix
> transparency #1 95 target r
> save chromophores_with_B_cartoon.png supersample 5 height 2000
> ~cartoon
> save chromophores_without_cartoon.png supersample 5 height 2000
executed all_chromophores_and_quinones.cxc
> cartoon /BA-BX&helix
> select clear
> select /BP,BQ
992 atoms, 1032 bonds, 8 pseudobonds, 87 residues, 2 models selected
> open "C:/Users/tic20/OneDrive - University of
> Cambridge/Figures/Figure_4/all_chromophores_and_quinones.cxc"
> lighting full depthCue false
> graphics silhouettes true color grey
> ~cartoon #1
> show #1 models
> hide #2,4 models
> hide
> color B800 hotpink
> color B816 limegreen
> color B868 royalblue
> color :FE orange
> color :MQ8 lime
> color :BPH orange
> color :CRT gold
> color /L:1001|/M:1005 red
> color /L:1003|/M:1003 blue
> setattr :HEC bonds radius 0.5
Assigning radius attribute to 184 items
> setattr ~:HEC bonds radius 0.25
Assigning radius attribute to 57836 items
> style @FE,MG sphere
Changed 113 atom styles
> show B800|B816|B868|:GPC,CRT,Fe,HEC,MQ8,BPH,BCL
> view matrix camera
> 0.72553,-0.59683,0.34262,402.85,0.68702,0.65722,-0.30997,18.517,-0.040173,0.46027,0.88687,723.18
> zoom pixelSize 0.212
> cartoon /BA-BX&helix
> transparency #1 95 target r
> save chromophores_with_B_cartoon.png supersample 5 height 2000
> transparency /BP,BQ 0 target r
> save chromophores_with_B_cartoon_1_and_24_opaque.png supersample 5 height
> 2000
> ~cartoon
> save chromophores_without_cartoon.png supersample 5 height 2000
executed all_chromophores_and_quinones.cxc
> select clear
> open "C:/Users/tic20/OneDrive - University of
> Cambridge/Figures/Figure_4/all_chromophores_and_quinones.cxc"
> lighting full depthCue false
> graphics silhouettes true color grey
> ~cartoon #1
> show #1 models
> hide #2,4 models
> hide
> color B800 hotpink
> color B816 limegreen
> color B868 royalblue
> color :FE orange
> color :MQ8 lime
> color :BPH orange
> color :CRT gold
> color /L:1001|/M:1005 red
> color /L:1003|/M:1003 blue
> setattr :HEC bonds radius 0.5
Assigning radius attribute to 184 items
> setattr ~:HEC bonds radius 0.25
Assigning radius attribute to 57836 items
> style @FE,MG sphere
Changed 113 atom styles
> show B800|B816|B868|:GPC,CRT,Fe,HEC,MQ8,BPH,BCL
> view matrix camera
> 0.72553,-0.59683,0.34262,402.85,0.68702,0.65722,-0.30997,18.517,-0.040173,0.46027,0.88687,723.18
> zoom pixelSize 0.212
> cartoon /BA-BX&helix
> transparency #1 95 target r
> save chromophores_with_B_cartoon.png supersample 5 height 2000
> transparency /BP,BQ 0 target r
> save chromophores_with_B_cartoon_1_and_24_opaque.png supersample 5 height
> 2000
> ~cartoon
> save chromophores_without_cartoon.png supersample 5 height 2000
executed all_chromophores_and_quinones.cxc
> select /BP,BQ
992 atoms, 1032 bonds, 8 pseudobonds, 87 residues, 2 models selected
> show :CDL
> color :CDL black
> show :CD4
> cartoon
> show :PGW
> show :LMY,LMZ,PEX
> surface protein
> color #1 fromatoms target s
> ui tool show "Side View"
> select clear
> ~surface
> surface
> select clear
> select clear
> ~surface
> surface
> select clear
> roll x 180 1
> roll x 180 1
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
53 atoms, 54 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 53 atom styles
> roll x 180 1
> ~surface
> surface
> select clear
> select clear
> clip list
Using 1 clip planes:
near offset -12.532, axis 0.026,0.102,0.994, point 190,200.4,197.6)
> select clear
> clip near 0 axis 0.026,0.102,0.994 position 190,200.4,197.6
> select clear
> clip near 0~surf axis 0.026,0.102,0.994 position 190,200.4,197.6
Invalid "near" argument: Expected 'off' or a number
> ~surface
> select clear
> select :MQ8
159 atoms, 162 bonds, 3 residues, 1 model selected
> surface
> clip near 0 axis 0.026,0.102,0.994 position 190,200.4,197.6
> select clear
> select /L:1022@C30
1 atom, 1 residue, 1 model selected
> select up
53 atoms, 54 bonds, 1 residue, 1 model selected
> usage surf
surface [atoms] [enclose an atoms specifier] [include an atoms specifier]
[probeRadius a number] [gridSpacing a number] [resolution a number] [level a
number] [color a color] [transparency a number] [visiblePatches an integer]
[sharpBoundaries true or false] [nthread an integer] [replace true or false]
[update true or false]
— create molecular surface
Subcommands are:
* surface cap
* surface check
* surface close
* surface dust
* surface hidePatches
* surface showPatches
* surface style
* surface undust
* surface unzone
* surface zone
> surface sel include sel
> surface /L include sel
> color /L fromatoms target s
> select clear
> surface /L
> select clear
> clip near -5 axis 0.026,0.102,0.994 position 190,200.4,197.6
> select :MQ8
159 atoms, 162 bonds, 3 residues, 1 model selected
> style sel sphere
Changed 159 atom styles
> select clear
> clip near -10 axis 0.026,0.102,0.994 position 190,200.4,197.6
> clip near -15 axis 0.026,0.102,0.994 position 190,200.4,197.6
> clip near -5 axis 0.026,0.102,0.994 position 190,200.4,197.6
> select clear
> select :PGW,CDL,PEX,LMY,LMZ
1122 atoms, 1103 bonds, 24 residues, 1 model selected
> select :PGW,CD4,PEX,LMY,LMZ
1626 atoms, 1601 bonds, 30 residues, 1 model selected
> style sel sphere
Changed 1626 atom styles
> select clear
> color :PGW,CD4,PEX,LMY,LMZ white
> select clear
> select clear
> usage surf
surface [atoms] [enclose an atoms specifier] [include an atoms specifier]
[probeRadius a number] [gridSpacing a number] [resolution a number] [level a
number] [color a color] [transparency a number] [visiblePatches an integer]
[sharpBoundaries true or false] [nthread an integer] [replace true or false]
[update true or false]
— create molecular surface
Subcommands are:
* surface cap
* surface check
* surface close
* surface dust
* surface hidePatches
* surface showPatches
* surface style
* surface undust
* surface unzone
* surface zone
> surface :PGW,CD4,PEX,LMY,LMZ enclose :PGW,CD4,PEX,LMY,LMZ
> select clear
> surface :MQ8 enclose :MQ8
> color :MQ8 fromatoms target s
> clip near -5 axis 0.026,0.102,0.994 position 190,200.4,197.6
> clip near -4 axis 0.026,0.102,0.994 position 190,200.4,197.6
> clip near -5 axis 0.026,0.102,0.994 position 190,200.4,197.6
> ~clip
> clip near -5 axis 0.026,0.102,0.994 position 190,200.4,197.6
> select clear
> ~surface :MQ8
> select clear
> select :MQ8
159 atoms, 162 bonds, 3 residues, 1 model selected
> style sel stick
Changed 159 atom styles
> setattr sel bonds radius 0.6
Assigning radius attribute to 162 items
> select clear
> usage clip
clip [near near] [far far] [front front] [back back] [position center point]
[axis an axis vector] [coordinateSystem a coordinate-system]
— set clip planes
near: off or a number
far: off or a number
front: off or a number
back: off or a number
clip list
— List active clip planes
clip model models [clipping]
— Turn off clipping for individual models.
clipping: true or false
clip off
— Turn off all clip planes
> usage surf
surface [atoms] [enclose an atoms specifier] [include an atoms specifier]
[probeRadius a number] [gridSpacing a number] [resolution a number] [level a
number] [color a color] [transparency a number] [visiblePatches an integer]
[sharpBoundaries true or false] [nthread an integer] [replace true or false]
[update true or false]
— create molecular surface
Subcommands are:
* surface cap
* surface check
* surface close
* surface dust
* surface hidePatches
* surface showPatches
* surface style
* surface undust
* surface unzone
* surface zone
> usage surf cap
surface cap [enable] [offset a number] [subdivision a number] [mesh true or
false]
— Enable or disable clipping surface caps
enable: true or false
> surface cap false
> surface cap true
> save C:\Users\tic20/Desktop_clip_cap_bug.jpg
> save C:\Users\tic20/Desktop/clip_cap_bug.jpg
Directory "C:\Users\tic20/Desktop" does not exist
> save C:\Users\tic20/Desktop/clip_cap_bug.jpg
Directory "C:\Users\tic20/Desktop" does not exist
> save C:\Users\tic20\OneDrive - University of
> "Cambridge\\\Desktop\\\clip_cap_bug.jpg"
Cannot determine format for 'C:\Users\tic20\OneDrive'
incomplete quoted text
> save C:\Users\tic20/clip_cap_bug.jpg
OpenGL version: 3.3.0 NVIDIA 426.00
OpenGL renderer: GeForce GTX 1070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUSTeK COMPUTER INC.
Model: GL502VS
OS: Microsoft Windows 10 Home (Build 19041)
Memory: 34,292,408,320
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-6700HQ CPU @ 2.60GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.8.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.6.20
chardet: 3.0.4
ChimeraX-AddH: 2.1.3
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.6.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.0.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.0
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.0
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.0
ChimeraX-Clipper: 0.15.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.1
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.0
ChimeraX-Help: 1.0
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.0
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-ISOLDE: 1.1.0
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.0
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Map: 1.0.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.1
ChimeraX-MDcrds: 2.0
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.0
ChimeraX-mmCIF: 2.2
ChimeraX-MMTF: 2.0
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.0
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.2.1
ChimeraX-PDB: 2.1
ChimeraX-PDBBio: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0
ChimeraX-PubChem: 2.0
ChimeraX-Read-Pbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.0
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.0.4
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.0
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.0
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.3
ChimeraX-uniprot: 2.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.20
decorator: 4.4.2
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
gdcm: 2.8.8
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.16
imagecodecs: 2020.5.30
imagecodecs-lite: 2020.1.31
imagesize: 1.2.0
ipykernel: 5.3.0
ipython: 7.15.0
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.3
jupyter-core: 4.6.3
kiwisolver: 1.2.0
line-profiler: 2.1.2
lxml: 4.5.1
MarkupSafe: 1.1.1
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msgpack: 1.0.0
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networkx: 2.4
numexpr: 2.7.1
numpy: 1.18.5+mkl
numpydoc: 1.0.0
openvr: 1.12.501
packaging: 20.4
parso: 0.7.1
pickleshare: 0.7.5
Pillow: 7.1.2
pip: 20.2.2
pkginfo: 1.5.0.1
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psutil: 5.7.0
pycollada: 0.7.1
pydicom: 2.0.0
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pyparsing: 2.4.7
PyQt5-commercial: 5.12.3
PyQt5-sip: 4.19.19
PyQtWebEngine-commercial: 5.12.1
python-dateutil: 2.8.1
pytz: 2020.1
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QtPy: 1.9.0
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requests: 2.24.0
scipy: 1.4.1
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six: 1.15.0
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Sphinx: 3.1.1
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sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
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WMI: 1.5.1
File attachment: clip_cap_bug.jpg
Attachments (1)
Change History (4)
by , 4 years ago
| Attachment: | clip_cap_bug.jpg added |
|---|
comment:1 by , 4 years ago
| Component: | Unassigned → Surface |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Cap colors not matching |
comment:2 by , 4 years ago
I realised the problem is that "color fromAtoms" sets the vertex_colors of the surface, but doesn't change the overall color property. Perhaps a reasonable compromise might be to set color to the average of vertex_colors?
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 26 April 2021 19:13
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #4566: Cap colors not matching (was: ChimeraX bug report submission)
#4566: Cap colors not matching
------------------------------------+-------------------------
Reporter: Tristan Croll | Owner: Tom Goddard
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Surface | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
------------------------------------+-------------------------
Changes (by Eric Pettersen):
* status: new => assigned
* component: Unassigned => Surface
* project: => ChimeraX
* platform: => all
* owner: (none) => Tom Goddard
--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4566#comment:1>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
follow-up: 2 comment:3 by , 4 years ago
| Type: | defect → enhancement |
|---|
Command color fromAtoms sets the colors of surface patches associated with the atoms. Clip caps don't have patches associated with atoms and so are not colored. The color zone command can be used to color clip caps. In the same vein "color fromAtoms" isn't going to color an EM or X-ray map with a fit atomic model because again the atoms do not have associated surface patches. Not sure how this might be improved. I don't think setting the single color of the cap makes sense. We might want fromAtoms to be smart and use color zone for caps. There might be another ticket on that topic.
At any rate, color fromAtoms is behaving as it was designed to behave in a simple if not ideal way.
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