id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7123 Basic Actions saving session: 'QEventLoop' object has no attribute 'exec_' marta.carroni@… Zach Pearson "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC) Description Nothing special, I have only updated chimerax to v 1.4 while the original session was generated with v 1.3 Log: UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. > open > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure3_ATPpocket_a.cxs Opened denmod_map_i4.ccp4 as #1, grid size 199,196,146, pixel 1.34, shown at level 0.12, step 1, values float32 Opened denmod_map_i4_copy.ccp4 as #2, grid size 199,196,146, pixel 1.34, shown at level 0.44, step 1, values float32 Opened denmod_map_i4_copy.ccp4 zone as #4, grid size 199,196,146, pixel 1.34, shown at level 0.572, step 1, values float32 Log from Sun Mar 27 22:51:28 2022UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. > open > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2c_overall.cxs Opened denmod_map_i4.ccp4 as #1, grid size 199,196,146, pixel 1.34, shown at level 0.12, step 1, values float32 Opened denmod_map_i4_copy.ccp4 as #2, grid size 199,196,146, pixel 1.34, shown at level 0.098, step 1, values float32 Log from Tue Mar 1 22:41:50 2022UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. > open > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2_bHairpinsP.cxs Opened denmod_map_i4.ccp4 as #1, grid size 199,196,146, pixel 1.34, shown at level 0.12, step 1, values float32 Opened denmod_map_i4_copy.ccp4 as #2, grid size 199,196,146, pixel 1.34, shown at level 0.098, step 1, values float32 Log from Tue Mar 1 18:09:05 2022UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. > open > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2_AGFcxs.cxs Opened denmod_map_i4.ccp4 as #1, grid size 199,196,146, pixel 1.34, shown at level 0.12, step 1, values float32 Opened denmod_map_i4_copy.ccp4 as #2, grid size 199,196,146, pixel 1.34, shown at level 0.098, step 1, values float32 Log from Fri Aug 13 11:00:00 2021UCSF ChimeraX version: 1.2.4 (2021-05-14) © 2016-2021 Regents of the University of California. All rights reserved. > open > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2_a_CT4.cxs Opened denmod_map_i4.ccp4 as #1, grid size 199,196,146, pixel 1.34, shown at level 0.12, step 1, values float32 Opened combined_refined_Ploops_cootren_Labcd_ATP_ADPs_A12_bstrandNterloops.pdb map 5 as #4, grid size 124,127,95, pixel 1.67, shown at level 0.11, step 1, values float32 Log from Fri Jun 18 15:39:00 2021UCSF ChimeraX version: 1.2.4 (2021-05-14) © 2016-2021 Regents of the University of California. All rights reserved. > open > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2cutvertical.cxs > format session Opened denmod_map_i4.ccp4 as #1, grid size 199,196,146, pixel 1.34, shown at level 0.1, step 1, values float32 Opened combined_refined_Ploops_cootren_Labcd_ATP_ADPs_A12_bstrandNterloops.pdb map 5 as #4, grid size 124,127,95, pixel 1.67, shown at level 0.11, step 1, values float32 Log from Mon Jun 7 22:54:12 2021UCSF ChimeraX version: 1.2.4 (2021-05-14) © 2016-2021 Regents of the University of California. All rights reserved. > open > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2.cxs Opened denmod_map_i4.ccp4 as #1, grid size 199,196,146, pixel 1.34, shown at level 0.1, step 1, values float32 Opened body001_masked_crown.mrc as #2.2, grid size 400,400,400, pixel 1.35, shown at level 0.0225, step 1, values float32 Opened combined_refined_Ploops_cootren_Labcd_ATP_ADPs_A12_bstrandNterloops.pdb map 5 as #4, grid size 124,127,95, pixel 1.67, shown at level 0.11, step 1, values float32 Log from Mon Jun 7 18:44:10 2021UCSF ChimeraX version: 1.2.4 (2021-05-14) © 2016-2021 Regents of the University of California. All rights reserved. > open > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2.cxs > format session Opened denmod_map_i4.ccp4 as #1, grid size 199,196,146, pixel 1.34, shown at level 0.12, step 1, values float32 Opened body001_masked_crown.mrc as #2.2, grid size 400,400,400, pixel 1.35, shown at level 0.0225, step 1, values float32 Opened combined_refined_Ploops_cootren_Labcd_ATP_ADPs_A12_bstrandNterloops.pdb map 5 as #4, grid size 124,127,95, pixel 1.67, shown at level 0.11, step 1, values float32 Log from Mon Jun 7 13:38:40 2021UCSF ChimeraX version: 1.2.4 (2021-05-14) © 2016-2021 Regents of the University of California. All rights reserved. > open > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure1.cxs > format session Opened denmod_map_i4.ccp4 as #1, grid size 199,196,146, pixel 1.34, shown at level 0.12, step 1, values float32 Opened body001_masked_crown.mrc as #2.2, grid size 400,400,400, pixel 1.35, shown at level 0.0225, step 1, values float32 Opened combined_refined_Ploops_cootren_Labcd_ATP_ADPs_A12_bstrandNterloops.pdb map 5 as #4, grid size 124,127,95, pixel 1.67, shown at level 0.11, step 1, values float32 Log from Mon Jun 7 08:05:30 2021UCSF ChimeraX version: 1.2.4 (2021-05-14) © 2016-2021 Regents of the University of California. All rights reserved. > open > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure1.cxs Opened denmod_map_i4.ccp4 as #1, grid size 199,196,146, pixel 1.34, shown at level 0.085, step 1, values float32 Opened body001_masked_crown.mrc as #2.2, grid size 400,400,400, pixel 1.35, shown at level 0.0225, step 1, values float32 Opened combined_refined_Ploops_cootren_Labcd_ATP_ADPs_A12_bstrandNterloops.pdb map 5 as #4, grid size 124,127,95, pixel 1.67, shown at level 0.11, step 1, values float32 Log from Sun Jun 6 23:35:17 2021UCSF ChimeraX version: 1.2.4 (2021-05-14) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > set bgColor white > open > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/density_mod_phenix/ResolveCryoEM_3/denmod_map_i4.ccp4 Opened denmod_map_i4.ccp4 as #1, grid size 199,196,146, pixel 1.34, shown at level 0.263, step 1, values float32 > volume #1 level 0.085 > ui tool show ""Hide Dust"" > surface dust #1 size 8.04 > lighting full > surface dust #1 size 10 > surface dust #1 size 10 > save ../Documents/ClpCP_radiografia.png width 1600 height 1600 supersample 3 > transparentBackground true > open > /Users/marta.carroni/Documents/ClpCPA_rosa/Clps_Daris_map/body001_masked_PbestDari.mrc > /Users/marta.carroni/Documents/ClpCPA_rosa/Clps_Daris_map/body001_masked_crown.mrc Opened body001_masked_PbestDari.mrc as #2.1, grid size 400,400,400, pixel 1.35, shown at level 8.48e-06, step 2, values float32 Opened body001_masked_crown.mrc as #2.2, grid size 400,400,400, pixel 1.35, shown at level 1.02e-05, step 2, values float32 > volume #2.1 step 1 > volume #2.1 level 0.03791 > close #2.1 > volume #2.2 level 0.02248 > volume #2.2 step 1 > select #2.2 2 models selected > ~select #2.2 Nothing selected > toolshed show > ui mousemode right select > select #2.2 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #2.2,0.95243,0.28449,-0.10926,-23.172,-0.30406,0.91121,-0.27792,210.94,0.02049,0.29792,0.95437,-69.175 > view matrix models > #2.2,0.31072,0.32437,0.89344,-238.67,0.56388,0.69379,-0.44799,99.698,-0.76518,0.64299,0.032666,396.73 > view matrix models > #2.2,0.4619,0.61924,0.63498,-262.08,0.5366,0.37492,-0.75597,309.67,-0.70619,0.68991,-0.15911,440.36 > view matrix models > #2.2,0.60401,0.54486,0.58164,-260.16,0.42333,0.399,-0.81338,355.36,-0.67525,0.73752,0.010342,355.21 > view matrix models > #2.2,0.774,0.43541,0.45973,-230.41,0.25538,0.44972,-0.85588,402.96,-0.57941,0.77985,0.23689,232.46 > view matrix models > #2.2,0.71519,0.51369,0.47395,-241.13,0.15844,0.54129,-0.82577,392.94,-0.68074,0.66567,0.30574,264.85 > view matrix models > #2.2,0.68147,0.17566,0.71045,-229.45,0.32864,0.79393,-0.51154,159.99,-0.65391,0.58208,0.48331,213.36 > ui mousemode right ""move picked models"" > view matrix models > #2.2,0.68147,0.17566,0.71045,-221.14,0.32864,0.79393,-0.51154,155.43,-0.65391,0.58208,0.48331,213.34 > view matrix models > #2.2,0.68147,0.17566,0.71045,-142.1,0.32864,0.79393,-0.51154,143.34,-0.65391,0.58208,0.48331,143.22 > volume #1 style image region 0,0,72,198,195,72 step 1 showOutlineBox true > volume #1 region 0,0,0,198,195,145 step 1 > volume #1 region 0,0,0,198,195,145 step 1 > volume #1 level -0.03658,0 level 0.5295,0.8 level 1.338,1 > volume #1 level -0.03658,0 level 0.1251,0.7231 level 1.338,1 > volume #1 level -0.03658,0 level 0.1251,0.7231 level 0.6891,0.2923 > volume #1 showOutlineBox false > save ../Documents/ClpCP_radiografia.png width 1600 height 1600 supersample 3 > transparentBackground true > volume #1 level -0.03658,0 level 0.1251,0.7231 level 0.6997,0.8 > save ../Documents/ClpCP_radiografia.png width 1600 height 1600 supersample 3 > transparentBackground true > save ../Documents/ClpCP_radiografia.png width 1600 height 1600 supersample 3 > transparentBackground false > open > /Users/marta.carroni/Documents/ClpCPA_rosa/session_bodies_190117_semplified_allonC.pyc Python code was compiled for a different version of Python > volume #1 style surface > open > /Users/marta.carroni/Documents/ClpCPA_rosa/manuscript_parts/final_pdbs_nov2020/combined_refined_Ploops_cootren_Labcd_ATP_ADPs_A12_bstrandNterloops.pdb Chain information for combined_refined_Ploops_cootren_Labcd_ATP_ADPs_A12_bstrandNterloops.pdb #3 --- Chain | Description A C E N | No description available B G | No description available D | No description available F | No description available H M | No description available I | No description available J K | No description available L | No description available S | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available > hide atoms > show cartoons > ui tool show ""Model Panel"" > select #2 3 models selected > ~select #2 Nothing selected > hide #!1 models > select #3: .A-N Expected an objects specifier or a keyword > select #3:.A-N Expected an objects specifier or a keyword > select 3:.A-N Expected an objects specifier or a keyword > select add /A 2948 atoms, 2967 bonds, 191 residues, 1 model selected > select add /B 5865 atoms, 5903 bonds, 380 residues, 1 model selected > select add /C 8813 atoms, 8870 bonds, 571 residues, 1 model selected > select add /D 11700 atoms, 11775 bonds, 1 pseudobond, 758 residues, 2 models selected > select add /F 14574 atoms, 14667 bonds, 2 pseudobonds, 945 residues, 2 models selected > select add /G 17488 atoms, 17600 bonds, 2 pseudobonds, 1134 residues, 2 models selected > select add /G 17488 atoms, 17600 bonds, 2 pseudobonds, 1134 residues, 2 models selected > select add /H 20349 atoms, 20479 bonds, 3 pseudobonds, 1320 residues, 2 models selected > select add /I 23180 atoms, 23328 bonds, 4 pseudobonds, 1504 residues, 2 models selected > select add /L 26020 atoms, 26186 bonds, 5 pseudobonds, 1688 residues, 2 models selected > select add /M 28881 atoms, 29065 bonds, 6 pseudobonds, 1874 residues, 2 models selected > select add /N 31822 atoms, 32025 bonds, 6 pseudobonds, 2065 residues, 2 models selected > select add /B 31822 atoms, 32025 bonds, 6 pseudobonds, 2065 residues, 2 models selected > select add /C 31822 atoms, 32025 bonds, 6 pseudobonds, 2065 residues, 2 models selected > select add /M 31822 atoms, 32025 bonds, 6 pseudobonds, 2065 residues, 2 models selected > select add /K 34676 atoms, 34897 bonds, 7 pseudobonds, 2250 residues, 2 models selected > color (#!3 & sel) dark gray > select /a 4346 atoms, 4398 bonds, 5 pseudobonds, 546 residues, 2 models selected > select /E 2948 atoms, 2967 bonds, 191 residues, 1 model selected > color sel dark gray > select /S 82 atoms, 81 bonds, 8 residues, 1 model selected > color sel black > select /a 4346 atoms, 4398 bonds, 5 pseudobonds, 546 residues, 2 models selected > ui tool show ""Color Actions"" > color sel fire brick > select /b 4264 atoms, 4317 bonds, 6 pseudobonds, 532 residues, 2 models selected > color sel salmon > select /c 4434 atoms, 4488 bonds, 4 pseudobonds, 559 residues, 2 models selected > color sel gold > select /d 4136 atoms, 4187 bonds, 5 pseudobonds, 520 residues, 2 models selected > color sel olive drab > select /e 8166 atoms, 8213 bonds, 6 pseudobonds, 512 residues, 2 models selected > color sel light sky blue > color sel sky blue > color sel light sky blue > color sel sky blue > select /f 8278 atoms, 8325 bonds, 5 pseudobonds, 516 residues, 2 models selected > color sel dodger blue > select clear > select /J 2854 atoms, 2872 bonds, 1 pseudobond, 185 residues, 2 models selected > color (#!3 & sel) dark gray > select clear > open /Users/marta.carroni/Dropbox/chimera_sessions_ClpPCA/MD_ND_MecA.pdb MD_ND_MecA.pdb title: Structure of S.aureus CLPC In complex with meca [more info...] Chain information for MD_ND_MecA.pdb #4 --- Chain | Description C I O U a m | class III stress response-related atpase, aaa+ superfamily E K Q W c o | atp-dependent CLP protease atp-binding subunit CLPC F L R X d p | atp-dependent CLP protease atp-binding subunit CLPC e f g h i j | adapter protein meca > select #4 5490 atoms, 5460 bonds, 6 pseudobonds, 1830 residues, 2 models selected > ui mousemode right ""move picked models"" > view matrix models #4,1,0,0,56.288,0,1,0,-60.01,0,0,1,25.306 > view matrix models #4,1,0,0,78.14,0,1,0,-87.575,0,0,1,52.561 > view matrix models #3,1,0,0,8.1169,0,1,0,-9.9621,0,0,1,8.992 > view matrix models #4,1,0,0,89.358,0,1,0,-107.73,0,0,1,91.076 > view matrix models #4,1,0,0,109.21,0,1,0,-127.66,0,0,1,94.941 > view matrix models #4,1,0,0,225.03,0,1,0,-11.788,0,0,1,55.494 > view matrix models #4,1,0,0,205.99,0,1,0,-26.324,0,0,1,61.327 > view matrix models #4,1,0,0,198.97,0,1,0,-30.061,0,0,1,63.242 > ui mousemode right ""move picked models"" > ui mousemode right select > select #4/L:20@CA 1 atom, 1 residue, 1 model selected > hide sel atoms > hide sel atoms > select #4/I:443@CA 1 atom, 1 residue, 1 model selected > select #4 5490 atoms, 5460 bonds, 6 pseudobonds, 1830 residues, 2 models selected > ~select #4 Nothing selected > select #4 5490 atoms, 5460 bonds, 6 pseudobonds, 1830 residues, 2 models selected > hide sel atoms > show sel cartoons > cartoon style (#!4 & sel) modeHelix tube sides 20 > preset cartoons/nucleotides cylinders/stubs Changed 79256 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs > show sel atoms > view sel > color sel bychain > hide #!4 models > view Drag select of 956 residues, 2 pseudobonds > select clear > ui mousemode right select > ui mousemode right translate > ui mousemode right zoom > ui mousemode right translate > preset ""overall look"" publication Preset expands to these ChimeraX commands: set bg white graphics silhouettes t > preset cartoons/nucleotides ribbons/slabs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > preset cartoons/nucleotides cylinders/stubs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs > preset cartoons/nucleotides licorice/ovals Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh default arrows f x round width 1 thick 1 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides tube/slab shape ellipsoid > show #!4 models > close #4 > preset ""initial styles"" ""original look"" Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset ""initial styles"" cartoon Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset ""molecular surfaces"" ""ghostly white"" Changed 0 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color white targ s trans 80 > preset ""overall look"" publication Preset expands to these ChimeraX commands: set bg white graphics silhouettes t > undo > undo > undo > undo Traceback (most recent call last): File ""/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/undo.py"", line 185, in undo inst.undo() File ""/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/undo.py"", line 522, in undo a.undo() File ""/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/undo.py"", line 396, in undo self._update_owner(owner, attribute, old_value, option, deleted_check) File ""/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/undo.py"", line 430, in _update_owner getattr(owner, attribute)(value) File ""/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/atomic/ribbon.py"", line 1939, in set_sheet_end_arrow self._set_gc_ribbon() File ""/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/atomic/ribbon.py"", line 2066, in _set_gc_ribbon s._graphics_changed |= s._RIBBON_CHANGE File ""/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/attributes.py"", line 61, in _getattr_ return base.__getattr__(self, attr_name, look_in_class=base) File ""/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/attributes.py"", line 57, in _getattr_ return look_in_class._attr_registration.get_attr(attr_name) File ""/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/attributes.py"", line 83, in get_attr raise AttributeError(""Execution of '%s' object's '%s' property raised AttributeError"" % (self.class_.__name__, attr_name)) from None AttributeError: Execution of 'Structure' object's '_graphics_changed' property raised AttributeError undo failed: Execution of 'Structure' object's '_graphics_changed' property raised AttributeError: AttributeError: Execution of 'Structure' object's '_graphics_changed' property raised AttributeError File ""/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/attributes.py"", line 83, in get_attr raise AttributeError(""Execution of '%s' object's '%s' property raised AttributeError"" % (self.class_.__name__, attr_name)) from None See log for complete Python traceback. > undo Traceback (most recent call last): File ""/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/undo.py"", line 185, in undo inst.undo() File ""/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/undo.py"", line 522, in undo a.undo() File ""/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/undo.py"", line 396, in undo self._update_owner(owner, attribute, old_value, option, deleted_check) File ""/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/undo.py"", line 434, in _update_owner getattr(owner, attribute)(*value) File ""/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/atomic/ribbon.py"", line 1864, in set_sheet_arrow_scale self._set_gc_ribbon() File ""/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/atomic/ribbon.py"", line 2066, in _set_gc_ribbon s._graphics_changed |= s._RIBBON_CHANGE File ""/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/attributes.py"", line 61, in _getattr_ return base.__getattr__(self, attr_name, look_in_class=base) File ""/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/attributes.py"", line 57, in _getattr_ return look_in_class._attr_registration.get_attr(attr_name) File ""/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/attributes.py"", line 83, in get_attr raise AttributeError(""Execution of '%s' object's '%s' property raised AttributeError"" % (self.class_.__name__, attr_name)) from None AttributeError: Execution of 'Structure' object's '_graphics_changed' property raised AttributeError undo failed: Execution of 'Structure' object's '_graphics_changed' property raised AttributeError: AttributeError: Execution of 'Structure' object's '_graphics_changed' property raised AttributeError File ""/Users/marta.carroni/Desktop/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/attributes.py"", line 83, in get_attr raise AttributeError(""Execution of '%s' object's '%s' property raised AttributeError"" % (self.class_.__name__, attr_name)) from None See log for complete Python traceback. > preset ""initial styles"" ""original look"" Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset cartoons/nucleotides ribbons/slabs Changed 73766 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > lighting full > lighting full > lighting soft > view > ui tool show ""Color Actions"" > ui windowfill toggle > ui windowfill toggle > select add/.A-N Expected an objects specifier or a keyword > select add /.A-N Expected an objects specifier or a keyword > select add /A 2948 atoms, 2967 bonds, 191 residues, 1 model selected > select add /A-N 40478 atoms, 40736 bonds, 8 pseudobonds, 2626 residues, 3 models selected > color (#!3 & sel) dark gray > select add /a 44824 atoms, 45134 bonds, 13 pseudobonds, 3172 residues, 16 models selected > select replace /a Expected an objects specifier or a keyword > select /a 4346 atoms, 4398 bonds, 5 pseudobonds, 546 residues, 2 models selected > colour /a red brick > color /a red brick Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > colour /a fire brick > colour /b salmon > colour /c gold > colour /d olive grab > color /d olive grab Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > colour /d olive drab > colour /e light blue > colour /f dodger blue > select clear > colour /S black > show #!1 models > ui mousemode right translate > ui tool show ""Fit in Map"" Fit molecule combined_refined_Ploops_cootren_Labcd_ATP_ADPs_A12_bstrandNterloops.pdb (#3) to map denmod_map_i4.ccp4 (#1) using 74184 atoms average map value = 0.01291, steps = 128 shifted from previous position = 2.44 rotated from previous position = 3.15 degrees atoms outside contour = 59923, contour level = 0.085 Position of combined_refined_Ploops_cootren_Labcd_ATP_ADPs_A12_bstrandNterloops.pdb (#3) relative to denmod_map_i4.ccp4 (#1) coordinates: Matrix rotation and translation 0.99909996 0.04219753 0.00431685 -4.93809295 -0.04202069 0.99850096 -0.03507283 11.57437078 -0.00579037 0.03485986 0.99937544 -0.99304355 Axis 0.63613447 0.09193917 -0.76608101 Axis point 274.64910232 103.03635904 0.00000000 Rotation angle (degrees) 3.15095997 Shift along axis -1.31640130 Opened combined_refined_Ploops_cootren_Labcd_ATP_ADPs_A12_bstrandNterloops.pdb map 5 as #4, grid size 124,127,95, pixel 1.67, shown at level 0.11, step 1, values float32 Fit map combined_refined_Ploops_cootren_Labcd_ATP_ADPs_A12_bstrandNterloops.pdb map 5 in map denmod_map_i4.ccp4 using 174685 points correlation = 0.471, correlation about mean = 0.6133, overlap = 7407 steps = 144, shift = 13.8, angle = 3.15 degrees Position of combined_refined_Ploops_cootren_Labcd_ATP_ADPs_A12_bstrandNterloops.pdb map 5 (#4) relative to denmod_map_i4.ccp4 (#1) coordinates: Matrix rotation and translation 0.99999997 -0.00010445 -0.00023506 0.04814859 0.00010438 0.99999995 -0.00030190 0.09674212 0.00023510 0.00030188 0.99999993 -0.16286802 Axis 0.76116794 -0.59271984 0.26326139 Axis point 0.00000000 484.12865811 195.55736650 Rotation angle (degrees) 0.02272424 Shift along axis -0.06356868 Average map value = 0.1906 for 74184 atoms, 29821 outside contour > view > ui windowfill toggle > view > color zone #1 near #3 distance 8.04 > select /a-f 33624 atoms, 33928 bonds, 31 pseudobonds, 3185 residues, 2 models selected > save > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure1.cxs ——— End of log from Sun Jun 6 23:35:17 2021 ——— opened ChimeraX session > select clear > turn x 90 > hide #!3 models > ui tool show ""Volume Viewer"" > ui tool show ""Side View"" > turn y 60 > undo > turn z 60 > turn z 60 > turn z 60 > surface cap mesh true > surface cap mesh false > surface cap subdivision 5.0 > surface cap subdivision 5.0 > surface cap subdivision 2.0 > surface cap subdivision 20.0 > surface cap subdivision 20.0 > surface cap false > surface cap true > surface cap mesh true Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic models, 1 maps. > show #!3 models > color zone #1 near #3 distance 8.04 > hide #!3 models > save > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure1.cxs > ui windowfill toggle > save ../Documents/ClpCP_aaa2fig1.png width 1600 height 1600 supersample 3 > transparentBackground true > ui windowfill toggle > ui mousemode right clip > ui mousemode right clip > ui mousemode right clip > ui tool show ""Side View"" > ui mousemode right clip > ui windowfill toggle > ui mousemode right select > ui mousemode right translate > view > save ../Documents/ClpCP_aaa1fig1.png width 1600 height 1600 supersample 3 > transparentBackground true > view > ui tool show ""Side View"" > select /a-f 33624 atoms, 33928 bonds, 31 pseudobonds, 3185 residues, 2 models selected Volume zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic models, 1 maps. > show #!3 models > volume zone #1 nearAtoms sel & #3 range 8.04 > hide #!3 models > ui windowfill toggle > lighting simple > lighting full > select /a-d 17180 atoms, 17390 bonds, 20 pseudobonds, 2157 residues, 2 models selected > show #!3 models > color zone #1 near sel & #3 distance 8.04 > undo > volume zone #1 nearAtoms sel & #3 range 8.04 > hide #!3 models > ui windowfill toggle > ui tool show ""Side View"" > volume #1 level 0.1 > ui windowfill toggle > ui tool show ""Surface Zone"" > surface zone #1 nearAtoms #3 distance 1.34 > show #!3 models > surface zone #1 nearAtoms #3 distance 1.34 > select /a-d 17180 atoms, 17390 bonds, 20 pseudobonds, 2157 residues, 2 models selected > surface zone #1 nearAtoms #3 distance 1.34 > surface zone #1 nearAtoms sel distance 1.34 > hide #!3 models > ui windowfill toggle > ui tool show ""Surface Zone"" > surface zone #1 nearAtoms sel distance 1.34 > surface zone #1 nearAtoms sel distance 2 > surface zone #1 nearAtoms sel distance 2 > select /a-d 17180 atoms, 17390 bonds, 20 pseudobonds, 2157 residues, 2 models selected > ui windowfill toggle > select /S 82 atoms, 81 bonds, 8 residues, 1 model selected > select add /S,a-d 17262 atoms, 17471 bonds, 20 pseudobonds, 2165 residues, 3 models selected > ui tool show ""Model Panel"" > show #!3 models > select add /S,a-d 17262 atoms, 17471 bonds, 20 pseudobonds, 2165 residues, 7 models selected > surface zone #1 nearAtoms sel distance 2 > hide #!3 models > ui windowfill toggle > surface dust #1 size 13.4 Volume zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic models, 1 maps. > select add /S,a-d 17262 atoms, 17471 bonds, 20 pseudobonds, 2165 residues, 7 models selected Volume zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic models, 1 maps. > ui tool show ""Model Panel"" > show #!3 models > volume zone #1 nearAtoms sel & #3 range 8.04 > hide #!3 models > ui windowfill toggle > volume #1 level 0.12 > ui windowfill toggle > ui tool show ""Hide Dust"" > surface dust #1 size 9.14 > surface dust #1 size 3 > surface dust #1 size 30 > surface dust #1 size 30 > select add /S,a-d 17262 atoms, 17471 bonds, 20 pseudobonds, 2165 residues, 7 models selected > show #!3 models > select add /S,a-d 17262 atoms, 17471 bonds, 20 pseudobonds, 2165 residues, 7 models selected > volume zone #1 nearAtoms sel & #3 range 8.04 > hide #!3 models > ui windowfill toggle > ui tool show ""Surface Zone"" > surface zone #1 nearAtoms sel distance 2 > ui windowfill toggle > ui tool show ""Hide Dust"" > select add /S,a-d 17262 atoms, 17471 bonds, 20 pseudobonds, 2165 residues, 7 models selected > surface dust #1 size 3.4 > surface dust #1 size 3.43 > surface dust #1 size 91.03 > surface dust #1 size 91.92 > surface dust #1 size 105.03 > ui windowfill toggle > preset ""overall look"" interactive Preset expands to these ChimeraX commands: ~set bg graphics silhouettes f > preset ""overall look"" publication Preset expands to these ChimeraX commands: set bg white graphics silhouettes t > save ../Documents/ClpCP_spiralfig1.png width 1600 height 1600 supersample 3 > transparentBackground true > save > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure1.cxs > view matrix camera position: 0.47201,0.8521,-0.22613,176.23,0.29575,-0.39468,-0.86992,-244.58,-0.83051,0.34373,-0.4383,-4.4071 model positions: #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,0.68147,0.17566,0.71045,-142.1,0.32864,0.79393,-0.51154,143.34,-0.65391,0.58208,0.48331,143.22,#2.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,-0.00010445,-0.00023506,0.048149,0.00010438,1,-0.0003019,0.096742,0.0002351,0.00030188,1,-0.16287,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#3.2,1,0,0,0,0,1,0,0,0,0,1,0,#3.3,1,0,0,0,0,1,0,0,0,0,1,0,#3.4,1,0,0,0,0,1,0,0,0,0,1,0,#3.5,1,0,0,0,0,1,0,0,0,0,1,0,#3.6,1,0,0,0,0,1,0,0,0,0,1,0,#3.7,1,0,0,0,0,1,0,0,0,0,1,0,#3.8,1,0,0,0,0,1,0,0,0,0,1,0,#3.9,1,0,0,0,0,1,0,0,0,0,1,0,#3.10,1,0,0,0,0,1,0,0,0,0,1,0,#3.11,1,0,0,0,0,1,0,0,0,0,1,0,#3.12,1,0,0,0,0,1,0,0,0,0,1,0,#3.13,1,0,0,0,0,1,0,0,0,0,1,0,#3.14,1,0,0,0,0,1,0,0,0,0,1,0,#3.15,1,0,0,0,0,1,0,0,0,0,1,0,#3.16,1,0,0,0,0,1,0,0,0,0,1,0,#3.17,1,0,0,0,0,1,0,0,0,0,1,0,#3.18,1,0,0,0,0,1,0,0,0,0,1,0,#3.19,1,0,0,0,0,1,0,0,0,0,1,0,#3.20,1,0,0,0,0,1,0,0,0,0,1,0,#3.21,1,0,0,0,0,1,0,0,0,0,1,0,#3.22,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,-0.00010445,-0.00023506,0.048149,0.00010438,1,-0.0003019,0.096742,0.0002351,0.00030188,1,-0.16287,#4.1,1,0,0,0,0,1,0,0,0,0,1,0 > ui windowfill toggle > view name spiral > save > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure1.cxs ——— End of log from Mon Jun 7 08:05:30 2021 ——— opened ChimeraX session > select /a 4346 atoms, 4398 bonds, 5 pseudobonds, 546 residues, 2 models selected > show #!3 models > color (#!3 & sel) orange red > select #3 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected > color zone #1 near sel & #3 distance 8.04 > ui tool show ""Model Panel"" > hide #!3 models > ~select #3 21 models selected > lighting simple > lighting full > ui tool show ""Side View"" > ui windowfill toggle > ui tool show ""Side View"" > show #!3 models > select #3 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected > color zone #1 near sel & #3 distance 8.04 > hide #!3 models > ~select #3 21 models selected > preset ""overall look"" publication Preset expands to these ChimeraX commands: set bg white graphics silhouettes t > graphics silhouettes false > save ../Documents/ClpCP_cut.png width 1600 height 1600 supersample 3 > transparentBackground true > view name cut > turn x 90 > ui tool show ""Surface Zone"" > surface unzone #1 > ui windowfill toggle > view name cut_horizontal > save ../Documents/ClpCP_cut_horizontal.png width 1600 height 1600 > supersample 3 transparentBackground true > save > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2.cxs ——— End of log from Mon Jun 7 13:38:40 2021 ——— opened ChimeraX session > view > select /S 82 atoms, 81 bonds, 8 residues, 1 model selected > ui tool show ""Color Actions"" > color sel lavender > ui tool show ""Model Panel"" > show #!3 models > color zone #1 near sel & #3 distance 8.04 > select #3 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected > select /A-N:1-20 3274 atoms, 3280 bonds, 8 pseudobonds, 218 residues, 2 models selected > color (#!3 & sel) dim gray > select #3 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected > ~select #3 21 models selected > color zone #1 near #3 distance 8.04 > surface dust #1 size 13.4 > volume #1 level 0.1 > open http://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup Opened http://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#startup > ui tool show ""Model Panel"" > select #3 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected > color zone #1 near sel & #3 distance 8.04 > hide #!3 target m > ui tool show ""Side View"" > show #!3 target m > color zone #1 near sel & #3 distance 8.04 > select /S 82 atoms, 81 bonds, 8 residues, 1 model selected > color (#!3 & sel) hot pink > select #3 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected > show #!3 target m > color zone #1 near sel & #3 distance 8.04 > hide #!3 models > select /S 82 atoms, 81 bonds, 8 residues, 1 model selected > color #1.1#!1-2 lime > select /S 82 atoms, 81 bonds, 8 residues, 1 model selected > show #!3 models > hide #!1 models > select #3 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected > ~select #3 21 models selected > select /S 82 atoms, 81 bonds, 8 residues, 1 model selected > ui tool show ""Color Actions"" > color sel light green > select #3 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected > ~select #3 21 models selected > select #3 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected > show #!1 models > color zone #1 near sel & #3 distance 8.04 > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > ~select #3 21 models selected > hide #!3 models > select /S 82 atoms, 81 bonds, 8 residues, 1 model selected > color #1.1#!1-2 magenta > show #!3 models > select /S 82 atoms, 81 bonds, 8 residues, 1 model selected > color (#!3 & sel) magenta > select #3 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected > color zone #1 near sel & #3 distance 8.04 > graphics silhouettes false > color zone #1 near sel & #3 distance 8.04 > ~select #3 21 models selected > hide #!3 models > turn y 10 > turn y 10 > turn y 10 > turn y -10 > turn y -10 > turn y -10 > ui tool show ""Model Panel"" > show #!3 models > hide #!1 models > select /A-N:98,123,172 560 atoms, 532 bonds, 42 residues, 1 model selected > style sel sphere Changed 560 atom styles > show sel atoms > color (#!3 & sel) hot pink > color (#!3 & sel) purple > select #3 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected > show #!1 models > color zone #1 near sel & #3 distance 8.04 > ~select #3 21 models selected > hide #!3 models > view name cut_vertical > matrix Unknown command: matrix > matrix list Unknown command: matrix list > save ../Documents/ClpCP_cut_vertical.png width 1600 height 1600 supersample > 3 transparentBackground true > turn x 90 > ui tool show ""Volume Viewer"" > ui tool show ""Side View"" > view name cut_horizontal > save ../Documents/ClpCP_cut_horizontal.png width 1600 height 1600 > supersample 3 transparentBackground true > save > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2.cxs ——— End of log from Mon Jun 7 18:44:10 2021 ——— opened ChimeraX session > select /a 4346 atoms, 4398 bonds, 5 pseudobonds, 546 residues, 2 models selected > show #!3 models > close #2 > ui tool show ""Color Actions"" > color sel fire brick > select #3 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected > color zone #1 near sel & #3 distance 8.04 > ~select #3 21 models selected > hide #!3 models > ui mousemode right zoom > ui mousemode right clip > ui mousemode right zoom > lighting full > lighting soft > lighting soft > lighting full > lighting soft > lighting full > graphics silhouettes true > lighting soft > lighting soft > graphics silhouettes false > lighting full > save ../Documents/ClpCP_cut_horizontal.png width 1600 height 1600 > supersample 3 transparentBackground true > save > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2cuthorizontal.cxs > turn x -90 > ui tool show ""Side View"" > select /A-N:1-20 3274 atoms, 3280 bonds, 8 pseudobonds, 218 residues, 2 models selected > show #!3 models > select #3 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected > select /A-N:1-20 3274 atoms, 3280 bonds, 8 pseudobonds, 218 residues, 2 models selected > color (#!3 & sel) dim gray > select #3 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected > color zone #1 near sel & #3 distance 8.04 > select /A-N:1-20 3274 atoms, 3280 bonds, 8 pseudobonds, 218 residues, 2 models selected > color (#!3 & sel) black > select #3 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected > color zone #1 near sel & #3 distance 8.04 > select /A-N:1-20 3274 atoms, 3280 bonds, 8 pseudobonds, 218 residues, 2 models selected > ui tool show ""Color Actions"" > color sel dim gray > select #3 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected > color zone #1 near sel & #3 distance 8.04 > hide #!3 models > ~select #3 21 models selected > select /A-N:98,123,172 560 atoms, 532 bonds, 42 residues, 1 model selected > show #!3 models > hide #!1 models > ui tool show ""Color Actions"" > color sel khaki > select #3 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected > show #!1 models > color zone #1 near sel & #3 distance 8.04 > select clear > select /A-N:98,123,172 560 atoms, 532 bonds, 42 residues, 1 model selected > ui tool show ""Color Actions"" > color sel violet > color sel lime > select #3 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected > color zone #1 near sel & #3 distance 8.04 > hide #!3 models > ~select #3 21 models selected > save ../Documents/ClpCP_cut_vertical.png width 1600 height 1600 supersample > 3 transparentBackground true > save > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2cutvertical.cxs ——— End of log from Mon Jun 7 22:54:12 2021 ——— opened ChimeraX session > lighting soft > lighting soft > lighting full > lighting full > graphics silhouettes true > surface cap false > surface cap true > surface cap mesh true > surface cap mesh false > show #!3 models > select #3 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected > color zone #1 near sel & #3 distance 8.04 > ~select #3 21 models selected > hide #!3 models > turn x 90 > hide #!1 models > show #!3 models > select /N,A,B,C,D,E,F:1-10 872 atoms, 872 bonds, 60 residues, 1 model selected > select /N,A,B,C,D,E,F:10-16 621 atoms, 613 bonds, 1 pseudobond, 41 residues, 2 models selected > color /N,A,B,C,D,E,F:10-16 redorange Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color sele redorange Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color /N,A,B,C,D,E,F:10-16 orangered > select clear > show #!1 models > color zone #1 near #3 distance 8.04 > ui tool show ""Side View"" > graphics silhouettes false > lighting shadows false > view > view start Expected an objects specifier or a view name or a keyword > view start Expected an objects specifier or a view name or a keyword > view start Expected an objects specifier or a view name or a keyword > view #1 start Expected an integer >= 1 or a keyword > lighting full > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > clip near 40 > clip near -40 > clip near -20 > clip near 10 > clip far -30 > clip far -30 > clip far -10 > clip far -10 > select #1 5 models selected > ~select #1 Nothing selected > select #3 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected > color zone #1 near sel & #3 distance 8.04 > ~select #3 21 models selected > hide #!3 models > show #!3 models > select #3 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected > select clear > hide #!3 models > view name cutcontact > save > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2_a_CT1.cxs > includeMaps true > ui windowfill toggle > ui windowfill toggle > color zone #5 near #2 distance 8.78 > wait 40 > color zone #5 near #2 distance 8.78 > wait 40 > color zone #5 near #2 distance 8.78 > wait 40 > color zone #5 near #2 distance 8.78 > wait 40 > color zone #5 near #2 distance 8.78 > wait 40 > color zone #5 near #2 distance 8.78 > wait 40 > color zone #5 near #2 distance 8.78 > wait 40 > save /Users/marta.carroni/Desktop/image8.png supersample 3 > save /Documents/PCA_Figure2a_cut.png png 1600 1600 300 supersample 3 > transparentBackground true Expected a keyword > save ../Documents/PCA_Figure2a_cut.png png 1600 1600 300 supersample 3 > transparentBackground true Expected a keyword > save ../Documents/PCA_Figure2a_cut.png png 1600 1600 300 supersample 3 > transparentBackground true Expected a keyword > save ../Documents/PCA_Figure2a_cut.png format png width 1600 height 1600 > supersample 3 transparentBackground true > save > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2_a_CT1.cxs > show #!3 models > hide #!1 models > select #3/A-N 40478 atoms, 40736 bonds, 8 pseudobonds, 2626 residues, 2 models selected > ui tool show ""Surface Zone"" > surface zone #1 nearAtoms #3 distance 8.04 > undo move Expected fewer arguments > view start Expected an objects specifier or a view name or a keyword > view list Named views: cut, cut_horizontal, cut_vertical, cutcontact, spiral > view cut > tunx x 90 Unknown command: tunx x 90 > tun x 90 Unknown command: tun x 90 > tun x 90 Unknown command: tun x 90 > show #!1 models > select #3 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected > ~select #3 Nothing selected > tun x 90 Unknown command: tun x 90 > turn x 90 > ui tool show ""Side View"" > clip near far 20 20 Invalid ""near"" argument: Expected 'off' or a number > clip near -20 far -20 > clip near 20 far 20 > clip near 20 far 20 > select #3/A-N 40478 atoms, 40736 bonds, 8 pseudobonds, 2626 residues, 2 models selected > surface zone #1 nearAtoms sele distance 8.04list Invalid ""nearAtoms"" argument: invalid atoms specifier > surface zone #1 nearAtoms #3/A-N distance 8.04list Invalid ""distance"" argument: Expected a number > surface zone #1 nearAtoms #3/A-N distance 8.04 > select clear > hide #!3 models > select #3/A-N 40478 atoms, 40736 bonds, 8 pseudobonds, 2626 residues, 2 models selected Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic models, 1 maps. > show #!3 models > select #3/A-N 40478 atoms, 40736 bonds, 8 pseudobonds, 2626 residues, 2 models selected > color zone #1 near sel & #3 distance 8.04 > hide #!3 models > clip near 20 far 20 > clip near -20 far -20 > clip near -20 far -20 > clip near -5 far -5 > select #3/A-N:10-16 1030 atoms, 1010 bonds, 6 pseudobonds, 66 residues, 2 models selected > show #!3 models > select #3/A-N 40478 atoms, 40736 bonds, 8 pseudobonds, 2626 residues, 2 models selected > select #3/A-N 40478 atoms, 40736 bonds, 8 pseudobonds, 2626 residues, 2 models selected > color zone #1 near sel & #3 distance 8.04 > color zone #1 near sel distance 3 > select #3 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected > ~select #3 21 models selected > hide #!3 models > clip near -5 far 10 > select #3/A-N 40478 atoms, 40736 bonds, 8 pseudobonds, 2626 residues, 2 models selected > color zone #1 near sel distance 3 > select #3/A-N 40478 atoms, 40736 bonds, 8 pseudobonds, 2626 residues, 2 models selected > color zone #1 near sel distance 8 > color zone #1 near sel distance 5 > color zone #1 near sel distance 4 > clip near 10 > color zone #1 near sel distance 3 > color zone #1 near sel distance 5 > color zone #1 near sel distance 8 > ui tool show ""Side View"" > ui tool show ""Volume Viewer"" > volume #1 level 0.12 > volume #1 level 0.125 > clip near -10 > volume #1 level 0.12 > color zone #1 near sel distance 3 > color zone #1 near sel distance 3 > color zone #1 near sel distance 3 > color zone #1 near sel distance 5 > color zone #1 near sel distance 3 > select #3 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected > ~select #3 21 models selected > select #3 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected > show #!3 models > color zone #1 near sel distance 3 > ~select #3 21 models selected > hide #!3 models > save ../Documents/PCA_Figure2a_cut2.png format png width 1600 height 1600 > supersample 3 transparentBackground true > save > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2_a_CT2.cxs > ui tool show ""Side View"" > show #!3 models > select #3/a-f:671-673 71 atoms, 69 bonds, 9 residues, 1 model selected > style (#!3 & sel) sphere Changed 71 atom styles > show (#!3 & sel) target ab > select #3/a-f:660-670,674-685 1059 atoms, 1058 bonds, 2 pseudobonds, 102 residues, 2 models selected > show (#!3 & sel) target ab > style (#!3 & sel) stick Changed 1059 atom styles > hide #3! ribbons Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide #3 ribbons > select clear > select #3/A,B,C,D,E,F,N 20463 atoms, 20594 bonds, 2 pseudobonds, 1327 residues, 2 models selected > color zone #1 near sel & #3 distance 8.04 > clip far -10 > clip far 10 > clip far 10 > clip near -10 > clip near -10 > select #3/A-N:10-16 1030 atoms, 1010 bonds, 6 pseudobonds, 66 residues, 2 models selected > color zone #1 near sel & #3 distance 8.04 > color zone #1 near sel & #3 distance 4 > color zone #1 near sel & #3 distance 8.04 > color zone #1 near sel & #3 distance 4 > clip near -10 > clip near -10 > ui tool show ""Side View"" > select #3/a-f:665-675 452 atoms, 453 bonds, 42 residues, 1 model selected > select #3/a-f:665-674 452 atoms, 453 bonds, 42 residues, 1 model selected > select #3/a-f:669-674 203 atoms, 205 bonds, 19 residues, 1 model selected > select #3/a-f:669-673 203 atoms, 205 bonds, 19 residues, 1 model selected > style (#!3 & sel) sphere Changed 203 atom styles > select clear > graphics silhouettes true > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting full > lighting full > lighting soft > lighting simple > lighting soft > lighting full > lighting full > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > ui windowfill toggle > undo > select clear > zoom 0.85 > ui tool show ""Side View"" > zoom -0.85 > view > zoom -1.5 > view > zoom 1.5 > ui tool show ""Side View"" > clip near 10 far -10 clip far plane is in front of near plane > clip near 10 far 10 clip far plane is in front of near plane > clip near 10 far 10 clip far plane is in front of near plane > clip near -10 far -10 clip far plane is in front of near plane > clip near -10 far -10 clip far plane is in front of near plane > clip near -10 far -10 clip far plane is in front of near plane > clip near -10 far -10 clip far plane is in front of near plane > clip far 10 clip far plane is in front of near plane > clip far 10 clip far plane is in front of near plane > clip far 10 > clip near -10 far -10 > clip near -10 far -10 > clip near -10 far -10 > clip far 10 > clip far 10 > clip far 10 > surface zone #1 nearAtoms #3/A-N distance 4 > zoom 1 > zoom 1.2 > zoom -1.2 > ui tool show ""Side View"" > view > zoom 1.5 > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > lighting full > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > clip near 20 > clip near -10 > clip near -10 > clip near -10 > clip near -10 > clip near -10 > clip near -10 > save ../Documents/PCA_Figure2a_cutPview.png format png width 1600 height > 1600 supersample 3 transparentBackground true > save > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2_a_CT3.cxs > save > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2_a_CT3.cxs > includeMaps true > graphics silhouettes false > save ../Documents/PCA_Figure2a_cutP2.png format png width 1600 height 1600 > supersample 3 transparentBackground true > select #3 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected > color zone #1 near sel & #3 distance 8.04 > surface unzone #1 > select clear > graphics silhouettes true > lighting shadows false > lighting shadows true > graphics silhouettes false > save ../Documents/PCA_Figure2a_cutP3.png format png width 1600 height 1600 > supersample 3 transparentBackground true > graphics silhouettes true > save ../Documents/PCA_Figure2a_cutP3s.png format png width 1600 height 1600 > supersample 3 transparentBackground true > save > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2_a_CT4.cxs > includeMaps true ——— End of log from Fri Jun 18 15:39:00 2021 ——— opened ChimeraX session > ui tool show ""Side View"" > view > select #3/A-N:98,127,172 420 atoms, 378 bonds, 42 residues, 1 model selected > hide (#!3 & sel) target a > color #3/A-N:29-72,186-197 magenta > select #3 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected > color zone #1 near sel & #3 distance 5 > select #3/A-N 40478 atoms, 40736 bonds, 8 pseudobonds, 2626 residues, 2 models selected > volume zone #1 nearAtoms sel & #3 range 8.04 > volume zone #1 nearAtoms sel & #3 range 8.04 > hide #1.1 models > show #1.1 models > hide #!3 models > show #!3 models > select clear > select #3/A-N 40478 atoms, 40736 bonds, 8 pseudobonds, 2626 residues, 2 models selected > volume zone #1 nearAtoms sel & #3 range 8.04 > volume zone #1 nearAtoms sel & #3 distance 5 Expected a keyword > volume zone #1 nearAtoms sel & #3 range 5 > select clear > select ::name=""LIG"" 336 atoms, 352 bonds, 8 residues, 1 model selected > hide sel target a > select #3/A-N 40478 atoms, 40736 bonds, 8 pseudobonds, 2626 residues, 2 models selected > volume zone #1 nearAtoms sel & #3 range 3 > select clear > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting flat > lighting flat > lighting full > lighting full > lighting soft > lighting soft > lighting simple > lighting simple > lighting soft > graphics silhouettes false > graphics silhouettes true > lighting full > lighting shadows false > lighting shadows true > lighting full > lighting soft > lighting simple > lighting simple > lighting full > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting full > lighting full > lighting soft > lighting flat > lighting flat > lighting flat > lighting full > lighting shadows false > lighting shadows true > lighting shadows false > lighting full > graphics silhouettes false > save > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2_c.cxs > includeMaps true > hide cartoons > graphics silhouettes true > graphics silhouettes false > save > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2_c1.cxs > includeMaps true > save /Users/marta.carroni/Desktop/image8.png supersample 3 > save ../Deskotop/Figure2c.png format png width 1600 height 1600 supersample > 3 transparentBackground true Directory ""../Deskotop"" does not exist > save ../Desktop/Figure2c.png format png width 1600 height 1600 supersample 3 > transparentBackground true > hide #!3 models > show #!3 models > select #3 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected > cartoon (#!3 & sel) > hide #!1 models > select #3/C,E:29-72,186-197 1550 atoms, 1556 bonds, 102 residues, 1 model selected > select #3/C,E:29-72 1332 atoms, 1338 bonds, 88 residues, 1 model selected > color #3/A-N:38-52,72-85,29-32,60-64,110-116,186-182 magenta > color #3/A-N:38-52,72-85,29-32,60-64,110-116,186-182,86-95 magenta > select clear > select #3 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected > select up 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 23 models selected > select up 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 27 models selected > select up 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 28 models selected > select up 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 28 models selected > color zone #1 near sel & #3 range 5 Expected a keyword > color zone #1 near sel & #3 distance 5 > show #!1 models > cartoon hide (#!3 & sel) > select clear > save > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2_c_suba.cxs > includeMaps true > save ../Deskotop/Figure2c_suba.png format png width 1600 height 1600 > supersample 3 transparentBackground true Directory ""../Deskotop"" does not exist > save ../Desktop/Figure2c_suba.png format png width 1600 height 1600 > supersample 3 transparentBackground true > view > save > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2_c_subb.cxs > includeMaps true > save ../Desktop/Figure2c_subb.png format png width 1600 height 1600 > supersample 3 transparentBackground true > view > save ../Desktop/Figure2c_subc.png format png width 1600 height 1600 > supersample 3 transparentBackground true > save > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2_c_subc.cxs > includeMaps true > view > save ../Desktop/Figure2c_subd.png format png width 1600 height 1600 > supersample 3 transparentBackground true > save > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2_c_subd.cxs > includeMaps true > view > save ../Desktop/Figure2c_sube.png format png width 1600 height 1600 > supersample 3 transparentBackground true > save > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2_c_sube.cxs > includeMaps true > view > view > view > select #3/a-f:671-673 71 atoms, 69 bonds, 9 residues, 1 model selected > hide #!4 models > close #4 > open > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/density_mod_phenix/ResolveCryoEM_3/denmod_map_i4_copy.ccp4 Opened denmod_map_i4_copy.ccp4 as #2, grid size 199,196,146, pixel 1.34, shown at level 0.263, step 1, values float32 > volume #2 level 0.05545 > volume #2 level 0.09802 > save > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2_AGFcxs.cxs > includeMaps true ——— End of log from Fri Aug 13 11:00:00 2021 ——— opened ChimeraX session > hide #!2 models > hide #!3 models > show #!3 models > select #3 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected > hide sel atoms > show sel cartoons > select clear > save > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2_bHairpinsP.cxs > includeMaps true ——— End of log from Tue Mar 1 18:09:05 2022 ——— opened ChimeraX session > lighting soft > lighting full > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > select #3/A:1-28 437 atoms, 439 bonds, 27 residues, 1 model selected > select #3/A-F,N:1-28 2907 atoms, 2919 bonds, 2 pseudobonds, 179 residues, 2 models selected > select ~sel 71277 atoms, 71826 bonds, 37 pseudobonds, 5640 residues, 7 models selected > hide sel cartoons > select #3/a-f 33624 atoms, 33928 bonds, 31 pseudobonds, 3185 residues, 2 models selected > show sel cartoons > select clear > view > lighting full > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > view > view orient > undo Drag select of 3355 residues, 25 pseudobonds > show sel surfaces > select clear > hide #!3 models > show #!3 models > ui tool show ""Side View"" > turn x 90 > turn y 60 > turn x 90 > hide #3.2 models > hide #3.3 models > hide #3.4 models > hide #3.5 models > hide #3.6 models > hide #3.7 models > hide #3.1 models > hide #3.15 models > hide #3.17 models > hide #3.18 models > hide #3.19 models > show #3.19 models > hide #3.19 models > hide #3.20 models > hide #3.21 models > hide #3.22 models > hide #!3 models > show #!3 models > view > show #3.1 models > hide #3.1 models > show #3.2 models > show #3.3 models > show #3.4 models > show #3.5 models > show #3.6 models > show #3.7 models > show #3.8 models > show #3.9 models > show #3.10 models > show #3.11 models > show #3.12 models > show #3.13 models > show #3.14 models > show #3.15 models > lighting shadows false > select #3/a-f 33624 atoms, 33928 bonds, 31 pseudobonds, 3185 residues, 2 models selected > ui tool show ""Basic Actions"" > hide /J target abp [Repeated 3 time(s)] > show /J target abp [Repeated 3 time(s)] > hide /J target abp [Repeated 1 time(s)] > cartoon style (#!3 & sel) modeHelix tube sides 20 > cartoon style (#!3 & sel) xsection oval modeHelix default > cartoon style (#!3 & sel & coil) xsection oval > cartoon style (#!3 & sel) xsection barbell modeHelix default > cartoon style (#!3 & sel) modeHelix tube sides 20 > select clear > save /Users/marta.carroni/Desktop/Figure2c_overall.png format png width 1600 > height 1600 supersample 3 transparentBackground true > save > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure2c_overall.cxs > includeMaps true ——— End of log from Tue Mar 1 22:41:50 2022 ——— opened ChimeraX session > cartoon style #3.2-15#!3 xsection oval modeHelix default > hide #!3 models > show #!3 models > select #3/a-f 33624 atoms, 33928 bonds, 31 pseudobonds, 3185 residues, 2 models selected > select ~sel 40560 atoms, 40817 bonds, 8 pseudobonds, 2634 residues, 7 models selected > hide sel cartoons > ~select #1 40560 atoms, 40817 bonds, 8 pseudobonds, 2634 residues, 19 models selected > select #3 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected > ~select #3.1 74184 atoms, 74745 bonds, 5819 residues, 22 models selected > select #3 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 2 models selected > ~select #3 21 models selected > hide #!3 models > show #!3 models > select #3/a-f 33624 atoms, 33928 bonds, 31 pseudobonds, 3185 residues, 2 models selected > select ~sel 40560 atoms, 40817 bonds, 8 pseudobonds, 2634 residues, 7 models selected > hide sel cartoons [Repeated 1 time(s)] > surface hidePatches (#!3 & sel) > select #3/a-f 33624 atoms, 33928 bonds, 31 pseudobonds, 3185 residues, 2 models selected > select #3/b/c/d/e/ Expected an objects specifier or a keyword > select #3/b,c,d,e 21000 atoms, 21205 bonds, 21 pseudobonds, 2123 residues, 2 models selected > hide sel cartoons > select #3/a:LIG 82 atoms, 86 bonds, 2 residues, 1 model selected > show sel atoms > select #3/f:704 24 atoms, 23 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 24 atom styles > show #!2 models > volume #2 style mesh > volume #!2 style mesh > undo > select clear > volume #2 level 0.2257 > volume #2 level 0.3162 > volume #2 level 0.3801 > select #3/a:LIG 82 atoms, 86 bonds, 2 residues, 1 model selected > hide sel atoms > select #3/a:LIG 82 atoms, 86 bonds, 2 residues, 1 model selected > volume zone #2 nearAtoms #3/a:LIG range 3 newMap true Opened denmod_map_i4_copy.ccp4 zone as #4, grid size 199,196,146, pixel 1.34, shown at step 1, values float32 > select up 4346 atoms, 4398 bonds, 546 residues, 1 model selected > select up 74184 atoms, 74745 bonds, 5819 residues, 2 models selected > select up 74184 atoms, 74745 bonds, 39 pseudobonds, 5819 residues, 23 models selected > select #3/f:704 24 atoms, 23 bonds, 1 residue, 1 model selected > color (#!3 & sel) byelement > volume #4 > volume #4 level 0.3929 > style sel ball Changed 24 atom styles > style sel sphere Changed 24 atom styles > style sel ball Changed 24 atom styles > mesh fine Unknown command: mesh fine > ui tool show ""Side View"" > volume #2 level 0.4404 > volume #4 level 0.5717 > select clear > ui mousemode right label > label #3/f:704 > ui mousemode right ""move label"" > label #4#3.2-15,23#!3 attribute label_one_letter_code > ui mousemode right label > ~label #4#3.2-15,23#!3 atoms > ~label #4#3.2-15,23#!3 residues > ui mousemode right label > label #3/f:704 > ui mousemode right ""move label"" > label #4#3.2-15,23#!3 attribute label_one_letter_code > label height 7 > label height 3 > ui mousemode right label > ~label #4#3.2-15,23#!3 residues > ui mousemode right label > label #3/f:704 > ui mousemode right ""move label"" > select clear > label #4#3.2-15,23#!3 text R704 Too many labels (5819), label texture size (2048,17496) exceeded maximum OpenGL texture size (16384), some labels will be blank. > ~label #4#3.2-15,23#!3 residues > save /Users/marta.carroni/Documents/figure3_ATP_suba.png width 1600 height > 1600 supersample 3 transparentBackground true > save > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure3_ATPpocket_a.cxs > volume #4 style surface > volume #4 color #b2b2b286 > volume #4 color #b2b2b24a > volume #4 color #b2b2b2c5 > volume #4 color #b2b2b241 > save /Users/marta.carroni/Documents/figure3_ATP_suba_v1.png width 1600 > height 1600 supersample 3 transparentBackground true > save > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure3_ATPpocket_a.cxs > includeMaps true ——— End of log from Sun Mar 27 22:51:28 2022 ——— opened ChimeraX session > hide hh Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide HH Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide HH atoms Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide hh Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide hh atoms Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hideh Unknown command: hideh > hidehh Unknown command: hidehh > hide hh Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > select N 7910 atoms, 5819 residues, 1 model selected > select H 28621 atoms, 3652 residues, 1 model selected > hide sel atoms > select clear > save /Users/marta.carroni/Documents/figure3a_pocketb.png width 1600 height > 1600 supersample 3 transparentBackground true > save > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure3_ATPpocket_a_I.cxs Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/basic_actions/tool.py"", line 225, in take_snapshot self.add_webview_state(data) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/basic_actions/tool.py"", line 260, in add_webview_state event_loop.exec_() AttributeError: 'QEventLoop' object has no attribute 'exec_' The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'tools' -> -> 'Basic Actions' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 896, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 625, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while saving session data for 'tools' -> -> 'Basic Actions' Populating font family aliases took 600 ms. Replace uses of missing font family "".AppleSystemUIFont"" with one that exists to avoid this cost. ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while saving session data for 'tools' -> -> 'Basic Actions' File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/basic_actions/tool.py"", line 225, in take_snapshot self.add_webview_state(data) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/basic_actions/tool.py"", line 260, in add_webview_state event_loop.exec_() AttributeError: 'QEventLoop' object has no attribute 'exec_' The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'tools' -> -> 'Basic Actions' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 116, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 51, in display run(session, cmd) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py"", line 90, in provider_save saver_info.save(session, path, **provider_kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core_formats/__init__.py"", line 84, in save return cxs_save(session, path, **kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 896, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 625, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while saving session data for 'tools' -> -> 'Basic Actions' ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while saving session data for 'tools' -> -> 'Basic Actions' File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. > save > /Users/marta.carroni/Documents/ClpCPA_rosa/better_filtering_ClpCP/session_figure3_ATPpocket_aI.cxs Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/basic_actions/tool.py"", line 225, in take_snapshot self.add_webview_state(data) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/basic_actions/tool.py"", line 260, in add_webview_state event_loop.exec_() AttributeError: 'QEventLoop' object has no attribute 'exec_' The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'tools' -> -> 'Basic Actions' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 896, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 625, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while saving session data for 'tools' -> -> 'Basic Actions' ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while saving session data for 'tools' -> -> 'Basic Actions' File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/basic_actions/tool.py"", line 225, in take_snapshot self.add_webview_state(data) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/basic_actions/tool.py"", line 260, in add_webview_state event_loop.exec_() AttributeError: 'QEventLoop' object has no attribute 'exec_' The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'tools' -> -> 'Basic Actions' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/toolbar/tool.py"", line 165, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 386, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/__init__.py"", line 1286, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/toolbar/__init__.py"", line 37, in run_provider providers.run_provider(session, name) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/toolbar/providers.py"", line 45, in run_provider what(session) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/toolbar/providers.py"", line 27, in _file_save show_save_file_dialog(session) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 51, in display run(session, cmd) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py"", line 90, in provider_save saver_info.save(session, path, **provider_kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core_formats/__init__.py"", line 84, in save return cxs_save(session, path, **kw) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 896, in save session.save(output, version=version, include_maps=include_maps) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 625, in save mgr.discovery(self._state_containers) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while saving session data for 'tools' -> -> 'Basic Actions' ValueError: error processing: 'tools' -> -> 'Basic Actions': Error while saving session data for 'tools' -> -> 'Basic Actions' File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. OpenGL version: 4.1 INTEL-18.7.4 OpenGL renderer: Intel(R) HD Graphics 615 OpenGL vendor: Intel Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Model Identifier: MacBook10,1 Processor Name: Dual-Core Intel Core i5 Processor Speed: 1,3 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 4 MB Hyper-Threading Technology: Enabled Memory: 8 GB System Firmware Version: 451.120.7.0.0 OS Loader Version: 540.120.3~6 SMC Version (system): 2.42f13 Software: System Software Overview: System Version: macOS 12.4 (21F79) Kernel Version: Darwin 21.5.0 Time since boot: 7:03 Graphics/Displays: Intel HD Graphics 615: Chipset Model: Intel HD Graphics 615 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x591e Revision ID: 0x0002 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2304 x 1440 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.10.8 cftime: 1.6.0 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.4.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.39.1 ChimeraX-AtomicLibrary: 7.0 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.7 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.1.5 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.5 ChimeraX-ModelPanel: 1.3.2 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.9 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.18.3 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.6.0 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.33.3 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.10.0 kiwisolver: 1.4.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.5 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openvr: 1.16.802 packaging: 21.0 ParmEd: 3.4.3 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.29 psutil: 5.9.0 ptyprocess: 0.7.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.0 PyQt6-Qt6: 6.3.0 PyQt6-sip: 13.3.1 PyQt6-WebEngine-commercial: 6.3.0 PyQt6-WebEngine-Qt6: 6.3.0 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 23.1.0 qtconsole: 5.3.0 QtPy: 2.1.0 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 }}} " defect closed normal Sessions fixed Tom Goddard Eric Pettersen all ChimeraX