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#3921 closed defect (duplicate)
Allow rainbow coloring on subsequences of a chain
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Depiction | Version: | |
| Keywords: | Cc: | Tom Goddard, Elaine Meng | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Darwin-19.6.0-x86_64-i386-64bit
ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
I cannot specify a group of residues when using the rainbow command. It colors everything in a rainbow rather than the specified atoms.
Log:
UCSF ChimeraX version: 1.1.1 (2020-10-07)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/gghanim/Desktop/RNASE H TEST.cxs"
Log from Sun Nov 8 14:07:33 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/gghanim/Library/Mobile
> Documents/com~apple~CloudDocs/Documents/Thesis Lab/Publications/2020 - P
> element Review/Figures/model_view_files/chimera files/model_view.cxs"
Log from Sun May 31 08:29:32 2020UCSF ChimeraX version: 0.93 (2020-04-03)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/gghanim/Library/Mobile
> Documents/com~apple~CloudDocs/Documents/Thesis Lab/Publications/2020 - P
> element Review/Figures/model_view_files/chimera files/model_view.cxs" format
> session
Log from Sun May 31 08:08:19 2020UCSF ChimeraX version: 0.93 (2020-04-03)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/gghanim/Library/Mobile
> Documents/com~apple~CloudDocs/Documents/Thesis Lab/Publications/2020 - P
> element Review/Figures/model_view_files/chimera files/model_view.cxs" format
> session
Log from Sun May 31 06:51:48 2020UCSF ChimeraX version: 0.93 (2020-04-03)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/gghanim/Library/Mobile
> Documents/com~apple~CloudDocs/Documents/Thesis Lab/Publications/2020 - P
> element Review/Figures/model_view_files/chimera files/model_view.cxs"
Log from Fri May 29 10:50:54 2020UCSF ChimeraX version: 0.93 (2020-04-03)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/gghanim/Library/Mobile
> Documents/com~apple~CloudDocs/Documents/Thesis Lab/Publications/2020 - P
> element Review/Figures/model_view_files/chimera files/model_view.cxs" format
> session
Log from Fri May 29 10:46:05 2020UCSF ChimeraX version: 0.93 (2020-04-03)
© 2016-2020 Regents of the University of California. All rights reserved.
> open2 "/Users/gghanim/Library/Mobile
> Documents/com~apple~CloudDocs/Documents/Thesis Lab/Publications/2020 - P
> element Review/Figures/model_view_files/chimera files/tnp_base.cxs"
Log from Tue May 12 11:19:53 2020UCSF ChimeraX version: 0.93 (2020-04-03)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/gghanim/Library/Mobile
> Documents/com~apple~CloudDocs/Documents/Thesis Lab/Publications/2020 - P
> element Review/Figures/DNA_view_files/chimera files/gtp_view_1.cxs"
Log from Sun May 10 16:50:57 2020UCSF ChimeraX version: 0.93 (2020-04-03)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/gghanim/Desktop/figure inspiration/tnp_base.cxs"
Log from Sun May 10 16:08:14 2020UCSF ChimeraX version: 0.93 (2020-04-03)
© 2016-2020 Regents of the University of California. All rights reserved.
> open2 "/Users/gghanim/Desktop/figure inspiration/gtp_view/gtp_view.cxs"
Log from Fri May 8 10:39:31 2020UCSF ChimeraX version: 0.93 (2020-04-03)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/gghanim/Desktop/TNP Glass Project/tnp.pdb" format PDB
Chain information for tnp.pdb
---
Chain | Description
1.2/A 1.3/A 1.2/G 1.3/G | No description available
1.2/B 1.3/B 1.2/H 1.3/H | No description available
1.1/C 1.4/C 1.1/I 1.4/I | No description available
1.1/D 1.4/D 1.1/J 1.4/J | No description available
1.1/E 1.4/E 1.1/K 1.4/K | No description available
> style stick
Changed 23912 atom styles
> nucleotides fill
> style nucleic stick
Changed 5580 atom styles
> nucleotides stubs
> show cartoons
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 652, in _rebuild_molecule
hide_residues = make_ladder(nd, residues, mol._ladder_params)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 1237, in make_ladder
va, na, ta = get_cylinder(params.rung_radius, ep0, ep1)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 733, in get_cylinder
h = distance(p0, p1)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 71, in distance
return sqrt(distance_squared(p, q))
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 63, in distance_squared
if len(p) == 3:
TypeError: object of type 'NoneType' has no len()
Error processing trigger "changes":
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 63, in distance_squared
if len(p) == 3:
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 652, in _rebuild_molecule
hide_residues = make_ladder(nd, residues, mol._ladder_params)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 1237, in make_ladder
va, na, ta = get_cylinder(params.rung_radius, ep0, ep1)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 733, in get_cylinder
h = distance(p0, p1)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 71, in distance
return sqrt(distance_squared(p, q))
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 63, in distance_squared
if len(p) == 3:
TypeError: object of type 'NoneType' has no len()
Error processing trigger "changes":
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 63, in distance_squared
if len(p) == 3:
See log for complete Python traceback.
> nucleotides fill
> style nucleic stick
Changed 5580 atom styles
> select #K
Expected an objects specifier or a keyword
> select #1.1.K
Expected an objects specifier or a keyword
> select #1.1/K
898 atoms, 1003 bonds, 2 pseudobonds, 2 models selected
> select #1.1.1-3/K
Nothing selected
> select #1.1:1-3/K
1217 atoms, 1358 bonds, 2 pseudobonds, 2 models selected
> select #1.1:1/K
1004 atoms, 1117 bonds, 2 pseudobonds, 2 models selected
> select #1.1/K:1
22 atoms, 24 bonds, 1 model selected
> select #1.1/K:1-17
349 atoms, 390 bonds, 1 model selected
> select #1.1/K:1-17/I
534 atoms, 597 bonds, 1 model selected
> select #1.1/K:1-17/I/C
719 atoms, 804 bonds, 1 model selected
> select #1.1/K:1-17/I/C/E:1-17
1068 atoms, 1194 bonds, 1 model selected
> name tdna sel
> select tdna
1068 atoms, 1194 bonds, 1 model selected
> select clear
> select tdna
Nothing selected
> select #1.1/K:1-17/I/C/E:1-17
1068 atoms, 1194 bonds, 1 model selected
> name list
tdna sel
> select #1.1/K:1-17/I/C/E:1-17
1068 atoms, 1194 bonds, 1 model selected
> name tdna #1.1/K:1-17/I/C/E:1-17
> select clear
> select tdna
1068 atoms, 1194 bonds, 1 model selected
> color tdna #5e4fa2
> select clear
> name frozen zip /D:128-150 /G:128-150
> name frozen hth /D:151-199 /G:151-199
> name frozen rnase /D:200-338,528-569 /G:200-338,528-569
> name frozen gbd /D:339-527 /G:339-527
> name frozen ctd /M:570-751 /U:570-751
nothing is selected by specifier
> name frozen ts /b/f/l:9-21 /k:9-21
> name frozen nts /a/e
> color name zip #5e4fa2
Color 'zip' is opaque, 36.86% red, 30.98% green, and 63.53% blue
> color name rnase #ffffbf
Color 'rnase' is opaque, 100% red, 100% green, and 74.9% blue
> color name hth #66c2a5
Color 'hth' is opaque, 40% red, 76.08% green, and 64.71% blue
> color name gtp #3288bd
Color 'gtp' is opaque, 19.61% red, 53.33% green, and 74.12% blue
> color name ctd #d53e4f
Color 'ctd' is opaque, 83.53% red, 24.31% green, and 30.98% blue
> color zip #5e4fa2
> color rnase #ffffbf
> color hth #66c2a5
> color gbd #3288bd
> color ctd #d53e4f
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color tdna #5e4fa2
> select clear
> name list
gbd [3052 atoms, 3100 bonds, 2 models]
hth [776 atoms, 798 bonds, 2 models]
nts [8932 atoms, 9286 bonds, 4 models]
rnase [2934 atoms, 3000 bonds, 2 models]
tdna #1.1/K:1-17/I/C/E:1-17
ts [2400 atoms, 2476 bonds, 4 models]
zip [374 atoms, 374 bonds, 2 models]
> select gbd
3052 atoms, 3100 bonds, 2 models selected
> name frozen gbd /D:339-527/G:339-527
> color gbd #3288bd
> select gbd
3052 atoms, 3100 bonds, 2 models selected
> select clear
> select /D:339-527/G:339-527
3052 atoms, 3100 bonds, 2 models selected
> select /A:339-527/G:339-527
6104 atoms, 6200 bonds, 2 models selected
> color gbd #3288bd
> name gbd /A:339-527/G:339-527
> color gbd #3288bd
> select clear
> name zip /A:128-150/G:128-150
> name hth /A:151-199/G:151-199
> name gbd /A:339-527/G:339-527
> name rnase /A:200-338,528-569/G:200-338,528-569
> name ctd /H:570-751/B:570-751
> name tdna /K:1-17/I/C/E:1-17
> color name zip #5e4fa2
Color 'zip' is opaque, 36.86% red, 30.98% green, and 63.53% blue
> color name rnase #ffffbf
Color 'rnase' is opaque, 100% red, 100% green, and 74.9% blue
> color name hth #66c2a5
Color 'hth' is opaque, 40% red, 76.08% green, and 64.71% blue
> color name gtp #3288bd
Color 'gtp' is opaque, 19.61% red, 53.33% green, and 74.12% blue
> color name ctd #d53e4f
Color 'ctd' is opaque, 83.53% red, 24.31% green, and 30.98% blue
> select ctd
3924 atoms, 3992 bonds, 2 models selected
> color zip #5e4fa2
> color rnase #ffffbf
> color hth #66c2a5
> color gbd #3288bd
> color ctd #d53e4f
> select clear
Empty filename passed to function
> save2 /Users/gghanim/Desktop/tnp.cxs
opened ChimeraX session
> set bgColor white
> name zip /A:128-150/G:128-150
> name hth /A:151-199/G:151-199
> name gbd /A:339-527/G:339-527
> name rnase /A:200-338,528-569/G:200-338,528-569
> name ctd /H:570-751/B:570-751
> name ts /E:-32--1/K:-32--1
> name nts /D/J
> name tdna /K:1-17/I/C/E:1-17
> name gtp #1.2/L #1.3/L
> color zip #ABACD7
> color rnase #FAD789
> color hth #DDECD7
> color gbd #CBE7FA
> color ctd #F1896B
> color tdna #6458A2
> color ts #B9D9A8
> color nts #F8F1A3
> graphics silhouettes true
> save2 "/Users/gghanim/Desktop/figure inspiration/tnp_base.cxs"
opened ChimeraX session
> select #1.2/F:1@O4'
1 atom, 1 model selected
> ui mousemode rightMode pivot
> select rnase
5868 atoms, 6000 bonds, 2 models selected
> hide sel target a
> hide sel cartoons
> select rnase
5868 atoms, 6000 bonds, 2 models selected
> show sel cartoons
> hide sel cartoons
> ui mousemode rightMode select
> select #1.1/D:1
22 atoms, 24 bonds, 1 model selected
> save2 "/Users/gghanim/Desktop/figure inspiration/gtp_view/gtp_view.cxs"
> hide sel atoms
> hide sel cartoons
> show sel cartoons
> show sel atoms
> style sel stick
Changed 22 atom styles
> style sel sphere
Changed 22 atom styles
> hide sel cartoons
> hide sel cartoons
> hide sel atoms
> toolshed show "Model Panel"
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.1 models
> show #!1.1 models
> hide #1.1.1 models
> show #1.1.1 models
> hide #1.2 models
> show #1.2 models
> hide #1.3 models
> show #1.3 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> hide #1.4.1 models
> hide #!1 models
> show #!1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #1.1.1 models
> show #1.1.1 models
> hide #1.1.1 models
> show #1.1.1 models
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> show #1.2 models
> hide #1.3 models
> show #1.3 models
> hide #1.3 models
> show #1.3 models
> hide #1.3 models
> show #1.4.1 models
> hide #1.4.1 models
> show #1.4.1 models
> hide #1.4.1 models
> show #1.4.1 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> hide #1.4.1 models
> close #1.4
> show #1.3 models
> hide #1.3 models
> show #1.3 models
> hide #1.3 models
> close #1.3
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> hide #1.1.1 models
> show #1.1.1 models
> hide #1.1.1 models
> hide #!1.1 models
> show #!1.1 models
> show #1.1.1 models
> show #1.2 models
> select rnase
2934 atoms, 3000 bonds, 1 model selected
> show sel atoms
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> select #1.2
9166 atoms, 9344 bonds, 1 model selected
> ~select #1.2
Nothing selected
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> show #1.2 models
> hide #1.1.1 models
> show #1.1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> select #1.1/E:-13
21 atoms, 22 bonds, 1 model selected
> hide sel
> hide sel cartoons
> select #1.1/E:-11
21 atoms, 23 bonds, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #1.2/G:454
8 atoms, 7 bonds, 1 model selected
> hide sel cartoons
> select :528,385,401,409,443,444,447,411|#1.1:-1
172 atoms, 164 bonds, 2 models selected
> select :528,385,401,409,443,444,409,401,443,447,411|#1.1:-1
172 atoms, 164 bonds, 2 models selected
> name gtpi :528,385,401,409,443,444,409,401,443,447,411|#1.1:-1
> select protein
9098 atoms, 9276 bonds, 1 model selected
> hide sel atoms
> show gtpi
> select clear
> color gtpi byhetero
> show surfaces
> close #1.2.1-4
> close #1.1.2-7
> select gtp zone 4
Expected a keyword
> select gtp zone<4
Expected a keyword
> select gtp :<4
210 atoms, 206 bonds, 2 models selected
> select gtp
34 atoms, 34 bonds, 1 model selected
> name gtp #1.2/L #1.3/L
> select gtp :<4
210 atoms, 206 bonds, 2 models selected
> select gtp
34 atoms, 34 bonds, 1 model selected
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> show #1.2 models
> select #1.2
9166 atoms, 9344 bonds, 1 model selected
> ~select #1.2
Nothing selected
> name gtp #1.2/F
> select gtp
34 atoms, 34 bonds, 1 model selected
> select gtp :<4
201 atoms, 197 bonds, 2 models selected
> show sel surfaces
> select gtp :<5
354 atoms, 356 bonds, 2 models selected
> show sel surfaces
> select clear
> select #1.1/E:-19@P
1 atom, 1 model selected
> hide sel surfaces
> select #1.1/E:-19@OP2
1 atom, 1 model selected
> hide sel surfaces
> select #1.1/E:-19@OP1
1 atom, 1 model selected
> hide sel surfaces
> select #1.1/E:-19@N3
1 atom, 1 model selected
> select #1.1/E:-19
19 atoms, 20 bonds, 1 model selected
> hide sel surfaces
> select clear
> show gbd
> show cartoons
> undo
> undo
> save2 "/Users/gghanim/Desktop/figure inspiration/gtp_view/gtp_view.cxs"
> select #1.2/G:449@NZ
1 atom, 1 model selected
> hide sel surfaces
> hide sel surfaces
> select gtpi
172 atoms, 164 bonds, 2 models selected
> select gtpi|gtp
206 atoms, 198 bonds, 2 models selected
> select ~sel
11750 atoms, 12264 bonds, 4 pseudobonds, 4 models selected
> color sel white
> color zip #ABACD7 target s
> color rnase #FAD789 target s
> color hth #DDECD7 target s
> color gbd #CBE7FA target s
> color ctd #F1896B target s
> color tdna #6458A2 target s
> color ts #B9D9A8 target s
> color nts #F8F1A3 target s
> color gbd #CBE7FA target s transparency 50
> color gbd #CBE7FA target s transparency 30
> color gbd #CBE7FA target s transparency 60
> color target s transparency 50
> color gbd #CBE7FA target s transparency 30
> color gbd #CBE7FA target s transparency 30
> color gbd #CBE7FA target s transparency 60
> color zip #ABACD7 target s transparency 60
> color rnase #FAD789 target s transparency 60
> color hth #DDECD7 target s transparency 60
> color gbd #CBE7FA target s transparency 50
> color ctd #F1896B target s transparency 60
> color tdna #6458A2 target s transparency 60
> color ts #B9D9A8 target s transparency 60
> color nts #F8F1A3 target s transparency 60
> select clear
> select gtpi|gtp
206 atoms, 198 bonds, 2 models selected
> select ~sel
11750 atoms, 12264 bonds, 4 pseudobonds, 4 models selected
> color white target a
> color sel white target a
> color sel white target b
> color sel white target c
> color sel white target r
> color sel white target abcpfl
> select clear
> graphics silhouettes false
> graphics silhouettes true
> select #1.2/G:527
9 atoms, 8 bonds, 1 model selected
> select clear
> select #1.2/G:527
9 atoms, 8 bonds, 1 model selected
> hide sel cartoons
> select clear
> select #1.2/G:526@CA
1 atom, 1 model selected
> hide sel surfaces
> select #1.2/G:341@CD
1 atom, 1 model selected
> hide sel surfaces
> select clear
> hide sel cartoons
> select #1.2/G:444@CB
1 atom, 1 model selected
> select clear
> graphics silhouettes width 3
> graphics silhouettes width 2
> graphics silhouettes width 3
> select gtpi&gbd
112 atoms, 102 bonds, 1 model selected
> select #1.1/E:-19
19 atoms, 20 bonds, 1 model selected
> hide sel cartoons
> hide sel atoms
> select clear
> save2 "/Users/gghanim/Desktop/figure inspiration/gtp_view/gtp_view_1.cxs"
opened ChimeraX session
> select cofr
Expected an objects specifier or a keyword
> select
11956 atoms, 12462 bonds, 4 pseudobonds, 4 models selected
> cofr
Center of rotation: 172.09 157.48 142.68 fixed
> select clear
> select
11956 atoms, 12462 bonds, 4 pseudobonds, 4 models selected
> show sel surfaces
> select clear
> select #1.2/F
34 atoms, 34 bonds, 1 model selected
> show sel surfaces
> hide sel surfaces
> select
11956 atoms, 12462 bonds, 4 pseudobonds, 4 models selected
> show sel cartoons
> hide sel atoms
> show sel atoms
> select protein
9098 atoms, 9276 bonds, 1 model selected
> hide sel atoms
> select clear
> color zip #ABACD7
> color rnase #FAD789
> color hth #DDECD7
> color gbd #CBE7FA
> color ctd #F1896B
> color tdna #6458A2
> color ts #B9D9A8
> color nts #F8F1A3
> select subtract
Nothing selected
> select surface
Expected an objects specifier or a keyword
> select tar s
Expected an objects specifier or a keyword
> color zip #ABACD7 target s transparency 60
> color rnase #FAD789 target s transparency 60
> color hth #DDECD7 target s transparency 60
> color gbd #CBE7FA target s transparency 60
> color ctd #F1896B target s transparency 60
> color tdna #6458A2 target s transparency 60
> color ts #B9D9A8 target s transparency 60
> color nts #F8F1A3 target s transparency 60
> select gtp
34 atoms, 34 bonds, 1 model selected
> select #1.2
9166 atoms, 9344 bonds, 1 model selected
> select #1.2/L
34 atoms, 34 bonds, 1 model selected
> select #1.2/L/F
68 atoms, 68 bonds, 1 model selected
> color grey sel
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel grey
> color sel dark grey
> color sel grey
> color sel byhetero
> select clear
> select up
Nothing selected
> select #1.2/L/F
68 atoms, 68 bonds, 1 model selected
> show sel surfaces
> select up
9166 atoms, 9344 bonds, 3 models selected
> select down
68 atoms, 68 bonds, 7 models selected
> color sel grey target s transparency 60
> select clear
> select
11956 atoms, 12462 bonds, 4 pseudobonds, 4 models selected
> cofr sel
> select clear
> save2 /Users/gghanim/Desktop/tnp_base.cxs
opened ChimeraX session
> open2 "/Users/gghanim/Library/Mobile
> Documents/com~apple~CloudDocs/Documents/Thesis Lab/Publications/2020 - P
> element Review/Figures/model_view_files/chimera files/emd_20254.map"
Opened emd_20254.map, grid size 256,256,256, pixel 1.16, shown at level
0.00239, step 1, values float32
> volume #2 level 0.03034
> hide surfaces
> volume #2 level 0.03879
> surface dust #2 size 2
> surface dust #2 size 3
> surface dust #2 size 4
> surface dust #2 size 2
> surface dust #2 size 3
> surface dust #2 size 2
> surface dust #2 size 3
> surface undust
Missing or invalid "surfaces" argument: empty atom specifier
> surface undust #2
> volume zone #2 nearAtoms #1 minimalBounds false bondPointSpacing 5 newMap
> true
> show #!2 models
> select #3
2 models selected
> select #2
2 models selected
> ~select #2
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> volume #3 level 0.03034
> volume #3 level 0.03229
> select up
Nothing selected
> select down
Nothing selected
> surface dust #2 size 3
> surface dust #3 size 3
> surface dust #3 size 2
> save2 "/Users/gghanim/Library/Mobile
> Documents/com~apple~CloudDocs/Documents/Thesis Lab/Publications/2020 - P
> element Review/Figures/model_view_files/chimera files/model_view.cxs"
opened ChimeraX session
> select #1.1.5 #1.1.7
624 atoms, 1 model selected
> volume zone #3 nearAtoms sel minimalBounds false bondPointSpacing 5 newMap
> true
> select #1.1.1
4 pseudobonds, 1 model selected
> ~select #1.1.1
Nothing selected
> select #1.1.1
4 pseudobonds, 1 model selected
> ~select #1.1.1
Nothing selected
> select #1.1.2
185 atoms, 1 model selected
> ~select #1.1.2
1 model selected
> select #1.1.3
898 atoms, 1 model selected
> ~select #1.1.3
1 model selected
> select #1.1.4
898 atoms, 1 model selected
> ~select #1.1.4
1 model selected
> ; #1.1.1 #1.1.3 #1.1.4
Incomplete command: segmentation
> select #1.1.1 #1.1.7
312 atoms, 4 pseudobonds, 2 models selected
> select #1.1.1 #1.1.3
898 atoms, 4 pseudobonds, 2 models selected
> select #1.1.1 #1.1.3 #1.1
2790 atoms, 3118 bonds, 4 pseudobonds, 2 models selected
> select #1.1.1 #1.1.3 #1.1.4
1796 atoms, 4 pseudobonds, 2 models selected
> volume zone #3 nearAtoms sel minimalBounds false bondPointSpacing 5 newMap
> true
> select clear
> hide #!5 models
> show #!5 models
> hide #!4 models
> volume #5 level 0.03104
> volume #5 level 0.03041
> select #1.1.1 #1.1.3 #1.1.4
1796 atoms, 4 pseudobonds, 2 models selected
> volume zone #3 nearAtoms sel minimalBounds false newMap true
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!5 target m
> show #!5 target m
> hide #!5 target m
> save2 "/Users/gghanim/Library/Mobile
> Documents/com~apple~CloudDocs/Documents/Thesis Lab/Publications/2020 - P
> element Review/Figures/model_view_files/chimera files/model_view.cxs"
opened ChimeraX session
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!5 models
> show #!5 models
> show #!6 models
> hide #1.1.2 models
> show #1.1.2 models
> hide #1.1.6 models
> show #1.1.6 models
> select #1.1.2
185 atoms, 1 model selected
> select #1.1.6
185 atoms, 1 model selected
> select up
2790 atoms, 3118 bonds, 2 models selected
> select down
185 atoms, 7 models selected
> select #1.1.6 #1.1.2
370 atoms, 1 model selected
> volume zone #3 nearAtoms sel minimalBounds false newMap true
> show #!4 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> close #4-7
> close #2
> show #!1 models
> select #1.1
2790 atoms, 3118 bonds, 4 pseudobonds, 2 models selected
> select clear
> save2 "/Users/gghanim/Library/Mobile
> Documents/com~apple~CloudDocs/Documents/Thesis Lab/Publications/2020 - P
> element Review/Figures/model_view_files/chimera files/model_view.cxs"
> show #!3 models
> volume #3 color #ffffb2fe
> volume #3 color #ffffb2f7
> volume #3 color #ffffb2ec
> volume #3 color #ffffb2d4
> volume #3 color #ffffb2c5
> volume #3 color #ffffb2b9
> volume #3 color #ffffb2ad
> volume #3 color #ffffb29a
> volume #3 color #ffffb293
> volume #3 color #ffffb28f
> volume #3 color #ffffb28b
> volume #3 color #ffffb285
> volume #3 color #ffffb27d
> volume #3 color #ffffb27c
> volume #3 color #ffffb27d
> volume #3 color #ffffb27e
> volume #3 color #ffffb280
> hide #!3 models
> hide #1.1.2 models
> show #1.1.2 models
> hide #1.1.2 models
> hide #1.1.6 models
> show #1.1.6 models
> show #1.1.2 models
> select #1.1/C #1.1/I
370 atoms, 414 bonds, 1 model selected
> volume zone #3 nearAtoms sel minimalBounds false newMap true
> select #1.1/E #1.1/K
1796 atoms, 2006 bonds, 4 pseudobonds, 2 models selected
> volume zone #3 nearAtoms sel minimalBounds false newMap true
> show #!3 models
> hide #!3 models
> select #1.1/D #1.1/J
624 atoms, 698 bonds, 1 model selected
> volume zone #3 nearAtoms sel minimalBounds false newMap true
> select clear
> hide #!4 models
> hide #!2 models
> volume zone #3 nearAtoms range 3 sel minimalbounds false newmap true
Invalid "nearAtoms" argument: invalid atoms specifier
> volume zone #3 nearAtoms sel range 3 minimalBounds false newMap true
no atoms specified for zone
> select #1.1/D #1.1/J
624 atoms, 698 bonds, 1 model selected
> volume zone #3 nearAtoms sel range 3 minimalBounds false newMap true
> hide #!5 models
> volume zone #3 nearAtoms sel range 2 minimalBounds false newMap true
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!2 models
> save2 "/Users/gghanim/Library/Mobile
> Documents/com~apple~CloudDocs/Documents/Thesis Lab/Publications/2020 - P
> element Review/Figures/model_view_files/chimera files/model_view.cxs"
opened ChimeraX session
> close #4
> close #2
> close #5
> close #6
> close #7
> volume zone #3 nearAtoms sel range 2.5 minimalBounds false newMap true
> close #2
> volume zone #3 nearAtoms sel range 2.5 minimalBounds false newMap true
> select #1.1/E #1.1/K
1796 atoms, 2006 bonds, 4 pseudobonds, 2 models selected
> volume zone #3 nearAtoms sel range 2.5 minimalBounds false newMap true
> close #4
> close #2
> volume zone #3 nearAtoms sel range 2 minimalBounds false newMap true
> select #1.1/D #1.1/J
624 atoms, 698 bonds, 1 model selected
> volume zone #3 nearAtoms sel range 2 minimalBounds false newMap true
> select up
2790 atoms, 3118 bonds, 3 models selected
> select up
2790 atoms, 3118 bonds, 4 pseudobonds, 8 models selected
> select #1.1/C #1.1/I
370 atoms, 414 bonds, 1 model selected
> volume zone #3 nearAtoms sel range 2 minimalBounds false newMap true
> select clear
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!3 models
> name
Missing or invalid "name" argument: Expected a text string
> name list
ctd /H:570-751/B:570-751
gbd /A:339-527/G:339-527
gtp #1.2/F
gtpi :528,385,401,409,443,444,409,401,443,447,411|#1.1:-1
hth /A:151-199/G:151-199
nts /D/J
rnase /A:200-338,528-569/G:200-338,528-569
tdna /K:1-17/I/C/E:1-17
ts /E:-32--1/K:-32--1
zip /A:128-150/G:128-150
> select rnase
2934 atoms, 3000 bonds, 1 model selected
> volume zone #3 nearAtoms sel range 2 minimalBounds false newMap true
> select ctd
1962 atoms, 1996 bonds, 1 model selected
> volume zone #3 nearAtoms sel range 2 minimalBounds false newMap true
> volume zone #3 nearAtoms hth range 2 minimalBounds false newMap true
> volume zone #3 nearAtoms zip range 2 minimalBounds false newMap true
> volume zone #3 nearAtoms gbd range 2 minimalBounds false newMap true
> volume zone #3 nearAtoms gtp range 2 minimalBounds false newMap true
> save2 "/Users/gghanim/Library/Mobile
> Documents/com~apple~CloudDocs/Documents/Thesis Lab/Publications/2020 - P
> element Review/Figures/model_view_files/chimera files/model_view.cxs"
> hide #!4 models
> hide #!5 models
> hide #!6 models
> show #!6 models
> color #8 #ABACD7
> show #!5 models
> show #!4 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!7 models
> show #!7 models
> hide #!8 models
> show #!8 models
> hide #!9 models
> show #!9 models
> color #9 #ABACD7
> hide #!5 models
> show #!5 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!8 models
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!11 models
> show #!11 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> show #!6 models
> color #5 #FAD789
> color #6 #FAD789
> color #8 #DDECD7
> hide #!11 models
> show #!11 models
> hide #!10 models
> show #!10 models
> color #10 #CBE7FA
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!8 models
> hide #!7 models
> show #!7 models
> color #7 #CBE7FA
> color #7 #F1896B
> save2 "/Users/gghanim/Library/Mobile
> Documents/com~apple~CloudDocs/Documents/Thesis Lab/Publications/2020 - P
> element Review/Figures/model_view_files/chimera files/model_view.cxs"
> hide #!9 models
> show #!9 models
> hide #!11 models
> show #!11 models
> hide #!10 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> select clear
> hide #!5 models
> show #!5 models
> color #5 #6458A2
> color #4 #F8F1A3
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!9 models
> hide #!9 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> close #11
> select ::name="GTP"
64 atoms, 68 bonds, 1 model selected
> name gtp sel
> volume zone #3 nearAtoms gtp range 2 minimalBounds false newMap true
> hide #!5 models
> select #1.2/L:3@MG
1 atom, 1 model selected
> volume zone #3 nearAtoms sel range 2 minimalBounds false newMap true
> show #!5 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> save2 "/Users/gghanim/Library/Mobile
> Documents/com~apple~CloudDocs/Documents/Thesis Lab/Publications/2020 - P
> element Review/Figures/model_view_files/chimera files/model_view.cxs"
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!4 models
> hide #!5 models
> select #1.1/K/E
1796 atoms, 2006 bonds, 4 pseudobonds, 2 models selected
> color zone #2 near sel distance 3
> show #!2 models
> save2 "/Users/gghanim/Library/Mobile
> Documents/com~apple~CloudDocs/Documents/Thesis Lab/Publications/2020 - P
> element Review/Figures/model_view_files/chimera files/model_view.cxs"
> hide #!11 models
> show #!11 models
> hide #!2 models
> select clear
> hide #!12 models
> select #1.2/B:676
9 atoms, 8 bonds, 1 model selected
> select #1.2/B:676
9 atoms, 8 bonds, 1 model selected
> select #1.2/B:676
9 atoms, 8 bonds, 1 model selected
> select clear
> select #1.2/L:3@MG
1 atom, 1 model selected
> name mg sel
> select clear
> style stick
Changed 11956 atom styles
> save2 "/Users/gghanim/Library/Mobile
> Documents/com~apple~CloudDocs/Documents/Thesis Lab/Publications/2020 - P
> element Review/Figures/model_view_files/chimera files/model_view.cxs"
> color zone #12 near mg distance 3
> show #!12 models
> hide #!12 models
> select mg
Nothing selected
> name list
ctd /H:570-751/B:570-751
gbd /A:339-527/G:339-527
gtp sel
gtpi :528,385,401,409,443,444,409,401,443,447,411|#1.1:-1
hth /A:151-199/G:151-199
mg sel
nts /D/J
rnase /A:200-338,528-569/G:200-338,528-569
tdna /K:1-17/I/C/E:1-17
ts /E:-32--1/K:-32--1
zip /A:128-150/G:128-150
> select mg
Nothing selected
> select #1.2/L:3@MG
1 atom, 1 model selected
> name mg sel
> select clear
> select mg
Nothing selected
> select #1.2/L:3@MG
1 atom, 1 model selected
> name mag sel
> select clear
> select mag
Nothing selected
> select #1.2/L
34 atoms, 34 bonds, 1 model selected
> select clear
> select #1.2/L 3
Expected a keyword
> select #1.2/L MG
Expected a keyword
> color zone #12 near sel distance 3
> show #!12 models
> hide #!12 models
> hide #!11 models
> show #!11 models
> select gtp
68 atoms, 1 model selected
> hide #!11 models
> select clear
> select gtp
Nothing selected
> select clear
> save2 "/Users/gghanim/Library/Mobile
> Documents/com~apple~CloudDocs/Documents/Thesis Lab/Publications/2020 - P
> element Review/Figures/model_view_files/chimera files/model_view.cxs"
> select gtp
Nothing selected
> select ::name="GTP"
64 atoms, 68 bonds, 1 model selected
> color zone #11 near sel distance 3
> show #!11 models
> show #!12 models
> show #!10 models
> show #!9 models
> show #!8 models
> show #!7 models
> show #!6 models
> show #!5 models
> show #!4 models
> show #!3 models
> show #!2 models
> hide #!1.2 models
> hide #!1.1 models
> hide #!1 models
> hide #!3 models
> lighting full
> save2 "/Users/gghanim/Library/Mobile
> Documents/com~apple~CloudDocs/Documents/Thesis Lab/Publications/2020 - P
> element Review/Figures/model_view_files/chimera files/model_view.cxs"
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> lighting full
> lighting soft
> lighting full
> lighting simple
> lighting soft
> lighting full
> lighting soft
> save2 "/Users/gghanim/Library/Mobile
> Documents/com~apple~CloudDocs/Documents/Thesis Lab/Publications/2020 - P
> element Review/Figures/model_view_files/chimera files/model_view.cxs"
> view orient
> view initial
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> lighting full
> lighting full
> lighting soft
> lighting full
> lighting soft
> lighting full
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting soft
> view orient
> view initial
> hide #!8 models
> show #!8 models
> volume #8 level 0.03353
> view orient
> view initial
> rotate x 90
Unknown command: rotate x 90
> turn x 90
> turn x -90
> turn x -90
> turn x 90
> turn y 90
> turn y -90
> turn z 5
> turn z -5
> turn z -5
> turn z -5
> turn z -5
> turn z -5
> turn z 3
> turn z 1
> turn x -90
> turn x 10
> turn x -10
> turn x 5
> turn x -5
> view name side
> turn x 90
> view name top
> volume #9 level 0.03023
> select #2 #3 #4 #5 #6 #7 #8 #9 #10 #11 #12
22 models selected
> surface dust sel size 3
> surface dust sel size 2
> surface dust sel size 3
> surface dust sel size 3.5
> surface dust sel size 3
> surface dust sel size 3.5
> surface dust sel size 3.6
> surface dust sel size 3.7
> surface dust sel size 4
> surface dust sel size 5
> surface dust sel size 6
> surface dust sel size 7
> surface dust sel size 8
> surface dust sel size 3
> surface dust sel size 3.5
> view top
> select clear
> save2 "/Users/gghanim/Library/Mobile
> Documents/com~apple~CloudDocs/Documents/Thesis Lab/Publications/2020 - P
> element Review/Figures/model_view_files/chimera files/model_view.cxs"
> view side
> view top
> view side
> view top
> view side
> view top
> volume #9 level 0.02875
> volume #6 level 0.03376
> view top
> save map_top format png supersample 9 transparentBackground true
> view side
> save map_side format png supersample 9 transparentBackground true
> save2 "/Users/gghanim/Library/Mobile
> Documents/com~apple~CloudDocs/Documents/Thesis Lab/Publications/2020 - P
> element Review/Figures/model_view_files/chimera files/map_view.cxs"
> save2 "/Users/gghanim/Library/Mobile
> Documents/com~apple~CloudDocs/Documents/Thesis Lab/Publications/2020 - P
> element Review/Figures/model_view_files/chimera files/model_view.cxs"
> hide #!2 models
> hide #!4 models
> hide #!5 models
> hide #!7 models
> hide #!6 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> show #!1 models
> show #!1.1 models
> show #!1.2 models
> lighting full
> lighting soft
> lighting full
> lighting flat
> lighting simple
> lighting soft
> lighting full
> lighting soft
> save2 "/Users/gghanim/Library/Mobile
> Documents/com~apple~CloudDocs/Documents/Thesis Lab/Publications/2020 - P
> element Review/Figures/model_view_files/chimera files/model_view.cxs"
> cartoon style modeHelix tube
> cartoon style protein width 2.5
> cartoon style protein width 2
> cartoon style protein width 2.2
> cartoon style protein width 2.3
> cartoon style protein width 2.3 thickness .5
> cartoon style protein width 2.3 thickness .6
> cartoon style protein width 2.3 thickness .7
> cartoon style protein width 2.3 thickness .7 radius 2
> cartoon style protein width 2.3 thickness .7 radius 3
> cartoon style protein width 2.3 thickness .7 radius 2.5
> cartoon style protein width 2.3 thickness .7 radius 2.2
> cartoon style protein width 2.3 thickness .7 radius 2.1
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> lighting full
> lighting shadows false
> lighting soft
> lighting soft
> cartoon style protein width 2.1 thickness .7 radius 2.1
> cartoon style protein width 2.1 thickness .6 radius 2.1
> select ::name="MG"
4 atoms, 1 model selected
> style sel sphere
Changed 4 atom styles
> select clear
> save2 "/Users/gghanim/Library/Mobile
> Documents/com~apple~CloudDocs/Documents/Thesis Lab/Publications/2020 - P
> element Review/Figures/model_view_files/chimera files/model_view.cxs"
opened ChimeraX session
> lighting qualityOfShadows fine msMapSize 10
> lighting qualityOfShadows fine msMapSize 100
> lighting qualityOfShadows fine msMapSize 1000
> lighting qualityOfShadows fine msMapSize 100
> lighting qualityOfShadows finer msMapSize 100
> lighting qualityOfShadows finer msMapSize 1000
> lighting qualityOfShadows finer msMapSize 10000
> lighting qualityOfShadows finer multiShadow 10 msMapSize 10000
> lighting qualityOfShadows finer multiShadow 100 msMapSize 10000
> lighting qualityOfShadows finer multiShadow 100 msMapSize 1000
> lighting qualityOfShadows finer multiShadow 100 msMapSize 100
> lighting qualityOfShadows finer multiShadow 1000 msMapSize 100
> lighting qualityOfShadows finer multiShadow 1000 msMapSize 1000
> lighting qualityOfShadows finer multiShadow 100 msMapSize 1000
> lighting qualityOfShadows finer multiShadow 1000 msMapSize 1000
> lighting qualityOfShadows finer multiShadow 1000 msMapSize 100
> lighting qualityOfShadows finer multiShadow 1000 msMapSize 10
> lighting qualityOfShadows finer multiShadow 10 msMapSize 1000
> lighting qualityOfShadows finer multiShadow 100 msMapSize 100
> lighting qualityOfShadows finer multiShadow 1000 msMapSize 1000
> lighting qualityOfShadows finer multiShadow 10000 msMapSize 10000
> lighting qualityOfShadows finer multiShadow 5000 msMapSize 5000
> lighting qualityOfShadows finer multiShadow 1000 msMapSize 5000
> lighting qualityOfShadows finer multiShadow 1000 msMapSize 1000
> lighting qualityOfShadows finer multiShadow 1000 msMapSize 10000
> lighting qualityOfShadows finer multiShadow 100 msMapSize 100
> lighting qualityOfShadows finer multiShadow 1000 msMapSize 1000
> view side
> lighting qualityOfShadows finer multiShadow 1000 msMapSize 1000 msDepthBias
> 0.02
> lighting qualityOfShadows finer multiShadow 1000 msMapSize 1000 msDepthBias
> 0.1
> lighting qualityOfShadows finer multiShadow 1000 msMapSize 1000 msDepthBias
> 0.001
> lighting qualityOfShadows finer multiShadow 1000 msMapSize 1000 msDepthBias
> 0.01
> show #!12 models
> show #!11 models
> show #!3 models
> hide #!3 models
> hide #!11 models
> hide #!12 models
> lighting qualityOfShadows fine multiShadow 1000 msMapSize 1000
> lighting qualityOfShadows coarse multiShadow 1000 msMapSize 1000
> view side
> lighting qualityOfShadows coarse multiShadow 1000 msMapSize 100
> lighting qualityOfShadows coarse multiShadow 100 msMapSize 100
> lighting qualityOfShadows coarse multiShadow 10 msMapSize 100
> lighting qualityOfShadows coarse multiShadow 10 msMapSize 10
> lighting qualityOfShadows coarse multiShadow 10 msMapSize 100
> lighting qualityOfShadows coarse multiShadow 50 msMapSize 100
> lighting qualityOfShadows coarse multiShadow 500 msMapSize 1000
> lighting qualityOfShadows coarse multiShadow 1000 msMapSize 1000
> lighting qualityOfShadows coarse multiShadow 500 msMapSize 1000
> save2 "/Users/gghanim/Library/Mobile
> Documents/com~apple~CloudDocs/Documents/Thesis Lab/Publications/2020 - P
> element Review/Figures/model_view_files/chimera files/model_view.cxs"
opened ChimeraX session
> graphics silhouettes false
> hide #!1.2 models
> hide #!1.1 models
> hide #!1 models
> show #!1 models
> show #!1.2 models
> select 200-568
Expected an objects specifier or a keyword
> select #1.2 200-568
Expected a keyword
> select :200-569
5986 atoms, 6104 bonds, 1 model selected
> select /A:200-569
2993 atoms, 3052 bonds, 1 model selected
> select ~sel
8963 atoms, 9410 bonds, 4 pseudobonds, 26 models selected
> cartoon hide (#!1.2 & sel)
> select clear
> select /A:200-569
2993 atoms, 3052 bonds, 1 model selected
> select ~sel
8963 atoms, 9410 bonds, 4 pseudobonds, 26 models selected
> hide (#!1.2 & sel) target a
> select #1.2/A:544
11 atoms, 11 bonds, 1 model selected
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> ui tool show "Side View"
> graphics silhouettes true
> graphics silhouettes false
> select /A:312-330
156 atoms, 162 bonds, 1 model selected
> select /A:305-330
205 atoms, 211 bonds, 1 model selected
> cartoon hide (#!1.2 & sel)
> select #1.2/A:331
10 atoms, 10 bonds, 1 model selected
> cartoon hide (#!1.2 & sel)
> select /A:275-296
186 atoms, 188 bonds, 1 model selected
> select #1.2/A:296
8 atoms, 7 bonds, 1 model selected
> select /A:275-296
186 atoms, 188 bonds, 1 model selected
> select /A:274-296
197 atoms, 200 bonds, 1 model selected
> select /A:275-295
178 atoms, 180 bonds, 1 model selected
> cartoon hide (#!1.2 & sel)
> cartoon (#!1.2 & sel)
> transparency (#!1.2 & sel) 50
> transparency sel 50 target c
> transparency sel 20 target c
> transparency sel 80 target c
> select clear
> graphics silhouettes true
> graphics silhouettes false
> transparency sel 90 target c
> transparency /A:275-295 90 target c
> graphics silhouettes true
> select /A:305-330
205 atoms, 211 bonds, 1 model selected
> cartoon (#!1.2 & sel)
> transparency sel /A:305-330 90 target c
Missing or invalid "percent" argument: Expected a number
> transparency /A:305-330 90 target c
> select clear
> transparency /A:305-331 90 target c
> select /A:305-331
215 atoms, 222 bonds, 1 model selected
> cartoon (#!1.2 & sel)
> select clear
> select /A:339-527
1526 atoms, 1550 bonds, 1 model selected
> surface (#!1.2 & sel)
> surface hidePatches (#!1.2 & sel)
> style sel sphere
Changed 1526 atom styles
> show (#!1.2 & sel) target ab
> hide sel atoms
> show sel surfaces
> hide #!1.2 models
> show #!1.2 models
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!3 models
> hide #2.1 models
> show #2.1 models
> hide #!2 models
> hide #10.1 models
> show #!10 models
> show #10.1 models
> hide #!10 models
> hide #10.1 models
> hide sel surfaces
> select clear
> select :200-339,527-569
2968 atoms, 3034 bonds, 1 model selected
> select :200-338,527-569
2952 atoms, 3018 bonds, 1 model selected
> rainbow sel
> rainbow :200-338,527-569
> rainbow :200-338,527-569 residues
> rainbow :200-338 residues
> select
11956 atoms, 12462 bonds, 4 pseudobonds, 28 models selected
> ~select
Nothing selected
> select #1.2/A:250-300
424 atoms, 434 bonds, 1 model selected
> rainbow
> rainbow sel
> rainbow #1.2/A:250-300
> save "/Users/gghanim/RNASE H TEST.cxs"
opened ChimeraX session
> rainbow #1.2/A:250-300
> select
11956 atoms, 12462 bonds, 4 pseudobonds, 1262 residues, 26 models selected
> cartoon (#!1.2 & sel)
> rainbow
> select ~sel
11532 atoms, 12028 bonds, 4 pseudobonds, 1211 residues, 26 models selected
> rainbow target c
> rainbow sel target c
> cartoon hide (#!1.2 & sel)
> rainbow sel target c
> cartoon (#!1.2 & sel)
> color sequential sel target c
> color sequential #1.2/A:250-300 residues target c
OpenGL version: 4.1 ATI-3.10.18
OpenGL renderer: AMD Radeon Pro 570X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac19,1
Processor Name: 6-Core Intel Core i5
Processor Speed: 3 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 9 MB
Memory: 16 GB
Boot ROM Version: 1037.140.50.0.0
SMC Version (system): 2.46f13
Software:
System Software Overview:
System Version: macOS 10.15.7 (19H15)
Kernel Version: Darwin 19.6.0
Time since boot: 1 day 2:02
Graphics/Displays:
Radeon Pro 570X:
Chipset Model: Radeon Pro 570X
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x67df
Revision ID: 0x00c5
ROM Revision: 113-D0008A-042
VBIOS Version: 113-D0008A14GL-003
EFI Driver Version: 01.B1.042
Metal: Supported, feature set macOS GPUFamily2 v1
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: 5120 x 2880 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
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
appnope: 0.1.0
Babel: 2.8.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.6.20
chardet: 3.0.4
ChimeraX-AddH: 2.1.1
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-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.1.1
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: 1.0
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.0
ChimeraX-IMOD: 1.0
ChimeraX-IO: 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
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
matplotlib: 3.2.1
msgpack: 1.0.0
netifaces: 0.10.9
networkx: 2.4
numexpr: 2.7.1
numpy: 1.18.5
numpydoc: 1.0.0
openvr: 1.12.501
packaging: 20.4
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.1.2
pip: 20.2.2
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.7
psutil: 5.7.0
ptyprocess: 0.6.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.6.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
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
pyzmq: 19.0.2
qtconsole: 4.7.4
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.4.1
setuptools: 49.4.0
sfftk-rw: 0.6.6.dev0
six: 1.15.0
snowballstemmer: 2.0.0
sortedcontainers: 2.2.2
Sphinx: 3.1.1
sphinxcontrib-applehelp: 1.0.2
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
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.6.3
tinyarray: 1.2.2
tornado: 6.0.4
traitlets: 5.0.4
urllib3: 1.25.10
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.34.2
Change History (14)
comment:1 by , 5 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Depiction |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Nucleotides: point is None |
comment:2 by , 5 years ago
The bug George is reporting is not the traceback, it is about rainbow coloring a subset of residues
"I cannot specify a group of residues when using the rainbow command. It colors everything in a rainbow rather than the specified atoms."
I confirm that this does not work correctly in the daily build and will try to fix it.
comment:3 by , 5 years ago
The documentation says "color sequential" applies to to entire chains.
"residues (default) – a different color for each residue in a biopolymer chain (always applies to entire chains)"
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/color.html#sequential
Not sure why. Seems like unexpected behavior.
comment:4 by , 5 years ago
| Cc: | added |
|---|
Color sequential is used to color N to C terminus of a protein chain so you can see the backbone path. I think it is an very rare use where you want to rainbow color just a subsequence of the residues. Maybe that would be useful for coloring a single domain. It is not clear what the coloring behavior should be when rainbow coloring a subsequence. Should it take colors red to blue from minimum to maximum residue number? What if the specified residues cover two intervals with a large gap in between. Should the colors advance as if the gap residues were colored, so perhaps the two intervals would appear all red and all blue. Or should the colors ignore the gap between the two intervals and for example jump from yellow at the end of the first interval to yellow at the beginning of the second interval.
Elaine do you think we should change the behavior of color sequential to act on fewer residues than a whole chain? Or is too obscure a use case?
follow-up: 5 comment:5 by , 5 years ago
I was going to say no need to change the rainbow command, because you can use "color byattr" with the residue attribute "number" ... unfortunately it does not currently work because the attribute is not registered for the purposes of this command. However, I talked to Eric and he can make the change to fix it in tomorrow's build. Then theoretically you could specify the range of residues in the command, e.g. something like color byattr r:number /A:1-50 palette rainbow As to what to do with numbering gaps, I think that is a somewhat orthogonal issue. What does it do now if there is a missing segment and thus a jump in numbering? It could just do the same thing. Elaine
comment:6 by , 5 years ago
Fixed color sequential to color only the specified residues.
Leaving the ticket open for the nucleotides error.
comment:7 by , 5 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
Can you tell us more about your ChimeraX installation? The version number reported in this ticket is 1.1.1, but the filenames are "/Applications/ChimeraX-0.93.app/..." If you were actually running 0.93, and the line numbers in the traceback match 0.9.3, then the nucleotides error was fixed in #3057, and a newer version should fix this problem. If you are actually running 1.1.1, then please submit a structure that reproduces the problem.
follow-up: 8 comment:8 by , 5 years ago
Hello, I’m not sure what this nucleotide error is! I was having issues with color sequential. Thank you, G —— PhD, Nguyen Group MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge, CB2 0QH On 10 Nov 2020, 3:17 AM +0000, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>, wrote:
follow-up: 9 comment:9 by , 5 years ago
Hi George, We saw a traceback related to the ChimeraX capability to display nucleic acids as rectangular slabs in the bug report you sent. I understand you are not concerned about that, but we probably have enough information from your bug report to find the source of that problem so others won't run into it. Tom
follow-up: 10 comment:10 by , 5 years ago
Hi Tom, I understand! At the time I was as using version 0.93 (May 10 2020). I’m currently using 1.1.1 and I have not seen this issue pop up. Please let me know how to proceed. G —— PhD, Nguyen Group MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge, CB2 0QH On 10 Nov 2020, 5:16 PM +0000, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>, wrote:
follow-up: 11 comment:11 by , 5 years ago
Ok. Possibly that nucleotides bug is already fixed. There is nothing you need to do. Greg Couch will look at the nucleotides error and decide if it was already fixed. For your actual request about rainbow coloring your command color sequential #1.2/A:250-300 residues target c will do what you wanted in today's ChimeraX daily build on the download page (below the 1.1 releases table).
follow-up: 12 comment:12 by , 5 years ago
Greg, the reason for the confusing Log traceback with ChimeraX-0.93.app paths in the traceback while the report was made with ChimeraX 1.1 is because a session was opened and sessions contain their own logs. This is pretty confusing when looking at the bug report Logs, since it does not show the boundary between old session logs and the current log. In the daily build I put in some code to mark the end of an old log with a line that indicates the end of a session log -- still kind of hard to see.
follow-up: 13 comment:13 by , 5 years ago
Forgot to push the code change, so this will be in tonight's ChimeraX daily build.
comment:14 by , 5 years ago
| Summary: | Nucleotides: point is None → Allow rainbow coloring on subsequences of a chain |
|---|
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Reported by George Ghanim