id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3921 Allow rainbow coloring on subsequences of a chain gghanim@… Greg Couch "{{{ 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 }}} " defect closed normal Depiction duplicate Tom Goddard Elaine Meng all ChimeraX