id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16739 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.1.1-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. 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===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/jessicakleiz/Library/Mobile > Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data > collection_CryoARM_VIB_SsCl > pH6.5/Map/CS_Jobs_LSN_Computer/J183/J183_004_volume_map_sharp.mrc.filepart"" Unrecognized file suffix '.filepart' > open ""/Users/jessicakleiz/Library/Mobile > Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data > collection_CryoARM_VIB_SsCl > pH6.5/Map/CS_Jobs_LSN_Computer/J183/J183_004_volume_map_sharp.mrc"" Opened J183_004_volume_map_sharp.mrc as #1, grid size 288,288,288, pixel 0.72, shown at level 0.219, step 2, values float32 > set bgColor white > open ""/Users/jessicakleiz/Library/Mobile > Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data > collection_CryoARM_VIB_SsCl > pH6.5/Map/CS_Jobs/J29/J29_004_volume_map_sharp.mrc"" Opened J29_004_volume_map_sharp.mrc as #2, grid size 256,256,256, pixel 0.731, shown at level 0.216, step 1, values float32 > volume flip #1 axis z Opened J183_004_volume_map_sharp.mrc z flip as #3, grid size 288,288,288, pixel 0.72, shown at step 1, values float32 > volume #2 color #ff9300 > volume #2 color #ff7e79 > volume #2 color #0096ff > volume #2 color #0433ff > volume #2 color #76d6ff > volume #2 color #0096ff > ui mousemode right ""translate selected models"" > select add #3 2 models selected > select subtract #3 Nothing selected > color #2 #0096ffff models > hide #!3 models > show #!3 models > select add #2 2 models selected > view matrix models #2,1,0,0,-40.053,0,1,0,-41.743,0,0,1,8.3809 > hide #!3 models > show #!1 models > select add #1 4 models selected > select subtract #2 2 models selected > view matrix models #1,1,0,0,-0.24923,0,1,0,0.05149,0,0,1,-1.3934 > view matrix models #1,1,0,0,-1.5195,0,1,0,-1.6505,0,0,1,-1.4552 > view matrix models #1,1,0,0,12.006,0,1,0,17.03,0,0,1,-2.7959 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.14178,0.97938,-0.14394,42.904,0.97101,0.10933,-0.21255,31.875,-0.19243,-0.16991,-0.96649,240.85 > view matrix models > #1,-0.94561,0.32488,-0.016346,179.72,0.32506,0.94564,-0.010153,-9.6302,0.012159,-0.014914,-0.99981,207.32 > ui tool show ""Side View"" > close #1 > open ""/Users/jessicakleiz/Library/Mobile > Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data > collection_CryoARM_VIB_SsCl > pH6.5/Doppio/job16/edited_coot/test_refined_edited_ISOLDE_4-coot-5.pdb"" Chain information for test_refined_edited_ISOLDE_4-coot-5.pdb #1 --- Chain | Description A | No description available > select add #1 5519 atoms, 5594 bonds, 1 pseudobond, 330 residues, 3 models selected > close #1 > close #3 > open ""/Users/jessicakleiz/Library/Mobile > Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data > collection_CryoARM_VIB_SsCl > pH6.5/Doppio/job16/edited_coot/test_refined_edited_ISOLDE_4-coot-4.pdb"" Chain information for test_refined_edited_ISOLDE_4-coot-4.pdb #1 --- Chain | Description A | No description available > close #2 > open ""/Users/jessicakleiz/Library/Mobile > Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data > collection_CryoARM_VIB_SsCl > pH6.5/Map/CS_Jobs/J29/J29_004_volume_map_sharp.mrc"" Opened J29_004_volume_map_sharp.mrc as #2, grid size 256,256,256, pixel 0.731, shown at level 0.216, step 1, values float32 Drag select of 1 residues, 2 J29_004_volume_map_sharp.mrc > view matrix models > #1,0.99915,-0.015001,0.038398,-2.3153,0.013039,0.99862,0.050869,-6.1317,-0.039108,-0.050325,0.99797,8.5737,#2,0.99915,-0.015001,0.038398,-2.3153,0.013039,0.99862,0.050869,-6.1317,-0.039108,-0.050325,0.99797,8.5737 > select add #2 11 atoms, 1 residue, 4 models selected > select add #1 5552 atoms, 5628 bonds, 332 residues, 4 models selected > select subtract #1 3 models selected > select add #1 5552 atoms, 5628 bonds, 332 residues, 4 models selected > select subtract #2 5552 atoms, 5628 bonds, 332 residues, 1 model selected > select subtract #1 Nothing selected > ui tool show ""Fit in Map"" > select 266-240 Expected an objects specifier or a keyword > select 266-240 Expected an objects specifier or a keyword > sel: 240-266 Unknown command: sel: 240-266 > sel:240-266 Unknown command: sel:240-266 > select : 240-266 419 atoms, 419 bonds, 27 residues, 1 model selected Opened test_refined_edited_ISOLDE_4-coot-4.pdb map 5 as #3, grid size 43,50,87, pixel 1.67, shown at level 0.0888, step 1, values float32 Opened test_refined_edited_ISOLDE_4-coot-4.pdb map 5 as #4, grid size 43,50,87, pixel 1.67, shown at level 0.0888, step 1, values float32 > fitmap #1 inMap #2 resolution 5 moveWholeMolecules false Fit map test_refined_edited_ISOLDE_4-coot-4.pdb map 5 in map J29_004_volume_map_sharp.mrc using 12228 points correlation = 0.894, correlation about mean = 0.6943, overlap = 808.4 steps = 44, shift = 0.0897, angle = 0.131 degrees Position of test_refined_edited_ISOLDE_4-coot-4.pdb map 5 (#4) relative to J29_004_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.99999804 -0.00193185 -0.00043150 0.14694904 0.00193235 0.99999748 0.00114485 -0.23057858 0.00042928 -0.00114568 0.99999925 0.10258373 Axis -0.50079531 -0.18819878 0.84485814 Axis point 113.94387319 90.58999761 0.00000000 Rotation angle (degrees) 0.13102948 Shift along axis 0.05647192 Average map value = 0.1985 for 5552 atoms, 3404 outside contour > isolde start > set selectionWidth 4 Done loading forcefield > isolde set simFidelityMode Medium/Medium ISOLDE: setting sim fidelity mode to Medium/Medium nonbonded_cutoff_distance = 0.900000 use_gbsa = True gbsa_cutoff = 1.100000 > select add #1 5552 atoms, 5628 bonds, 332 residues, 1 model selected > select subtract #1 Nothing selected ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 5 residues in model #1 to IUPAC-IUB standards. Opened test_refined_edited_ISOLDE_4-coot-4.pdb map 5 as #3, grid size 45,50,87, pixel 1.67, shown at level 0.0888, step 1, values float32 Chain information for test_refined_edited_ISOLDE_4-coot-4.pdb --- Chain | Description 1.2/A | No description available > clipper associate #2 toModel #1 Opened J29_004_volume_map_sharp.mrc as #1.1.1.1, grid size 256,256,256, pixel 0.731, shown at step 1, values float32 > view matrix models > #1.2,0.98105,-0.062145,-0.18354,26.128,-0.076075,0.74762,-0.65975,97.232,0.17822,0.66121,0.72873,-49.946 > undo > ui mousemode right select > volume #1.1.1.1 color #0433ff > volume #1.1.1.1 color #0433ffe5 > volume #1.1.1.1 color #0433ffe6 > select add #1.2 5552 atoms, 5628 bonds, 332 residues, 10 models selected > select add #1.2 5552 atoms, 5628 bonds, 332 residues, 10 models selected > select add #1.2 5552 atoms, 5628 bonds, 332 residues, 10 models selected > select add #1.2 5552 atoms, 5628 bonds, 332 residues, 10 models selected > select add #1 5552 atoms, 5628 bonds, 332 residues, 17 models selected > select add #1 5552 atoms, 5628 bonds, 332 residues, 17 models selected > select add #1 5552 atoms, 5628 bonds, 332 residues, 17 models selected > select subtract #1.3 5552 atoms, 5628 bonds, 332 residues, 16 models selected > select add #1.2 5552 atoms, 5628 bonds, 332 residues, 16 models selected > select clear Drag select of 1 atoms, 1 bonds > volume #!1.1.1.1 style surface > transparency #1.1.1.1.2 0 > volume #1.1.1.1 color #0433ff24 > volume #1.1.1.1 level 0.2145 Drag select of 1 atoms > show sel cartoons > hide sel atoms > show sel cartoons > hide sel atoms > show sel cartoons > style sel stick Changed 1 atom style > hide sel cartoons > show sel cartoons > select add #1.2 5552 atoms, 5628 bonds, 332 residues, 10 models selected > select add #1.2 5552 atoms, 5628 bonds, 332 residues, 10 models selected > hide sel atoms > show sel cartoons > select clear > select add #1.2 5552 atoms, 5628 bonds, 332 residues, 10 models selected > select add #1.2 5552 atoms, 5628 bonds, 332 residues, 10 models selected > select add #1 5552 atoms, 5628 bonds, 332 residues, 17 models selected > select add #1 5552 atoms, 5628 bonds, 332 residues, 17 models selected > select add #1 5552 atoms, 5628 bonds, 332 residues, 17 models selected > select add #1 5552 atoms, 5628 bonds, 332 residues, 17 models selected > select subtract #1.1 5552 atoms, 5628 bonds, 332 residues, 12 models selected > select add #1.2 5552 atoms, 5628 bonds, 332 residues, 12 models selected Drag select of 2 residues > select : 240-266 419 atoms, 419 bonds, 27 residues, 1 model selected > select : 240-266 419 atoms, 419 bonds, 27 residues, 1 model selected > isolde release torsions #1.2&sel > isolde release torsions #1.2 backbone false > close #1.2 Deleting atomic symmetry model... Deleting atomic symmetry model... > open ""/Users/jessicakleiz/Library/Mobile > Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data > collection_CryoARM_VIB_SsCl > pH6.5/Doppio/job16/edited_coot/test_refined_edited_ISOLDE_4-coot-4.pdb"" Chain information for test_refined_edited_ISOLDE_4-coot-4.pdb #2 --- Chain | Description A | No description available ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 5 residues in model #2 to IUPAC-IUB standards. Chain information for test_refined_edited_ISOLDE_4-coot-4.pdb --- Chain | Description 2.2/A | No description available Deleting atomic symmetry model... > select clear > volume #1.1.1.1 level 0.1375 > isolde restrain distances #2.2 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... Please select a single atom! > select all 5552 atoms, 5628 bonds, 332 residues, 21 models selected Please select a single atom! > isolde sim start /A ISOLDE: started sim > ui tool show ""Ramachandran Plot"" > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 12 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /A:153 ISOLDE: started sim > isolde pepflip /A:153 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:152 ISOLDE: started sim > isolde pepflip /A:152 > isolde cisflip /A:152 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:153 ISOLDE: started sim > isolde pepflip /A:153 Deleting atomic symmetry model... Deleting atomic symmetry model... > isolde pepflip /A:153 > isolde cisflip /A:153 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:152 ISOLDE: started sim Deleting atomic symmetry model... > isolde pepflip /A:152 > isolde cisflip /A:152 > isolde pepflip /A:152 > isolde pepflip /A:153 > isolde cisflip /A:153 > isolde pepflip /A:152 > isolde cisflip /A:152 > isolde pepflip /A:152 > isolde cisflip /A:152 > isolde pepflip /A:153 Unable to flip peptide bond after 50 rounds. Giving up. > isolde cisflip /A:152 > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:197 ISOLDE: started sim > isolde pepflip /A:197 > isolde cisflip /A:197 Deleting atomic symmetry model... > isolde pepflip /A:197 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /A:196 ISOLDE: started sim > isolde pepflip /A:196 > isolde pepflip #!2.2/A:196 > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde stepto next Deleting atomic symmetry model... > isolde stepto prev > isolde sim start /A:196 ISOLDE: started sim > isolde pepflip /A:196 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > save ""/Users/jessicakleiz/Library/Mobile > Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data > collection_CryoARM_VIB_SsCl > pH6.5/Doppio/job16/edited_coot/test_refined_edited_ISOLDE_4-coot-6.pdb"" > close Deleting atomic symmetry model... > open ""/Users/jessicakleiz/Library/Mobile > Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data > collection_CryoARM_VIB_SsCl pH6.5/Doppio/job26/refined.mmcif"" > ""/Users/jessicakleiz/Library/Mobile > Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data > collection_CryoARM_VIB_SsCl pH6.5/Doppio/job26/refined_expanded.mmcif"" > ""/Users/jessicakleiz/Library/Mobile > Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data > collection_CryoARM_VIB_SsCl pH6.5/Doppio/job26/sharpened_weighted.mrc"" Summary of feedback from opening /Users/jessicakleiz/Library/Mobile Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data collection_CryoARM_VIB_SsCl pH6.5/Doppio/job26/refined.mmcif --- warning | Unknown polymer entity '1' on line 27 Summary of feedback from opening /Users/jessicakleiz/Library/Mobile Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data collection_CryoARM_VIB_SsCl pH6.5/Doppio/job26/refined_expanded.mmcif --- warning | Unknown polymer entity '1' on line 27 Chain information for refined.mmcif #1 --- Chain | Description A | No description available Chain information for refined_expanded.mmcif #2 --- Chain | Description A B C D E | No description available Opened sharpened_weighted.mrc as #3, grid size 90,90,90, pixel 2.08, shown at level 1.51, step 1, values float32 > open ""/Users/jessicakleiz/Library/Mobile > Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data > collection_CryoARM_VIB_SsCl > pH6.5/Map/CS_Jobs/J29/J29_004_volume_map_sharp.mrc"" Opened J29_004_volume_map_sharp.mrc as #4, grid size 256,256,256, pixel 0.731, shown at level 0.216, step 1, values float32 > volume #4 level 0.2306 > color #2 #011993ff > color #2 #0433ffff > color #1 #ff2f92ff > color byhetero > style stick Changed 16734 atom styles > style stick Changed 16734 atom styles > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > volume #4 level 0.1836 > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > ui tool show ""Side View"" > isolde start > set selectionWidth 4 Done loading forcefield > isolde set simFidelityMode Medium/Medium ISOLDE: setting sim fidelity mode to Medium/Medium nonbonded_cutoff_distance = 0.900000 use_gbsa = True gbsa_cutoff = 1.100000 > ui tool show ""Ramachandran Plot"" ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 10 residues in model #2 to IUPAC-IUB standards. Chain information for refined_expanded.mmcif --- Chain | Description 2.2/A 2.2/B 2.2/C 2.2/D 2.2/E | No description available ISOLDE: created disulfide bonds between the following residues: A131-A145; A69-A115; D69-D115; E131-E145; B131-B145; D131-D145; C69-C115; E69-E115; C131-C145; B69-B115 Computing secondary structure > ui tool show ""Ramachandran Plot"" > clipper associate #4 toModel #2 Opened J29_004_volume_map_sharp.mrc as #2.1.1.1, grid size 256,256,256, pixel 0.731, shown at step 1, values float32 > ui tool show ""Ramachandran Plot"" > close > open ""/Users/jessicakleiz/Library/Mobile > Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data > collection_CryoARM_VIB_SsCl > pH6.5/Map/CS_Jobs/J29/J29_004_volume_map_sharp.mrc"" Opened J29_004_volume_map_sharp.mrc as #1, grid size 256,256,256, pixel 0.731, shown at level 0.216, step 1, values float32 > open ""/Users/jessicakleiz/Library/Mobile > Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data > collection_CryoARM_VIB_SsCl pH6.5/Doppio/job26/refined_expanded.pdb"" Chain information for refined_expanded.pdb #2 --- Chain | Description A B C D E | No description available > style stick Changed 13945 atom styles > isolde start > set selectionWidth 4 Done loading forcefield > isolde set simFidelityMode Medium/Medium ISOLDE: setting sim fidelity mode to Medium/Medium nonbonded_cutoff_distance = 0.900000 use_gbsa = True gbsa_cutoff = 1.100000 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 10 residues in model #2 to IUPAC-IUB standards. Chain information for refined_expanded.pdb --- Chain | Description 2.2/A 2.2/B 2.2/C 2.2/D 2.2/E | No description available ISOLDE: created disulfide bonds between the following residues: B131-B145; B69-B115; E69-E115; D131-D145; C131-C145; D69-D115; E131-E145; C69-C115 Computing secondary structure > clipper associate #1 toModel #2 Opened J29_004_volume_map_sharp.mrc as #2.1.1.1, grid size 256,256,256, pixel 0.731, shown at step 1, values float32 > hide #!2.2 models > show #!2.2 models > volume style surface > volume #2.1.1.1 color #2b772c > volume #2.1.1.1 color #2b772c4b > ui tool show ""Ramachandran Plot"" > volume #2.1.1.1 level 0.1359 > isolde sim start /C:226/D:288 Sim termination reason: None ISOLDE: stopped sim > addh #2.2 Summary of feedback from adding hydrogens to refined_expanded.pdb #2.2 --- warnings | Not adding hydrogens to /A ARG 21 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A GLU 76 CB because it is missing heavy-atom bond partners Not adding hydrogens to /B ARG 21 CB because it is missing heavy-atom bond partners Not adding hydrogens to /B GLU 76 CB because it is missing heavy-atom bond partners Not adding hydrogens to /C ARG 21 CB because it is missing heavy-atom bond partners 5 messages similar to the above omitted notes | Termini for refined_expanded.pdb (#2.2) chain A determined from SEQRES records Termini for refined_expanded.pdb (#2.2) chain B determined from SEQRES records Termini for refined_expanded.pdb (#2.2) chain C determined from SEQRES records Termini for refined_expanded.pdb (#2.2) chain D determined from SEQRES records Termini for refined_expanded.pdb (#2.2) chain E determined from SEQRES records Chain-initial residues that are actual N termini: /A ILE 4, /B ILE 4, /C ILE 4, /D ILE 4, /E ILE 4 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A LEU 335, /B LEU 335, /C LEU 335, /D LEU 335, /E LEU 335 Chain-final residues that are not actual C termini: 1230 hydrogen bonds 13815 hydrogens added > isolde restrain distances #2.2 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... > isolde sim start /C:223-229/D:285-291 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:288/E:226 ISOLDE: started sim > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start #!2.2/E:226 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:226/B:288 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /D:226/E:288 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:226/C:288 ISOLDE: started sim > volume #2.1.1.1 level 0.114 > volume #2.1.1.1 level 0.1234 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:269/E:177 ISOLDE: started sim > isolde pepflip /A:269 > isolde cisflip /A:269 > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:269 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /B:177/C:269 ISOLDE: started sim > volume #2.1.1.1 level 0.06526 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 3 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /C:269 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /A:177/B:269 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 5 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > volume #2.1.1.1 level 0.2271 > isolde sim start /D:177/E:269 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 4 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /C:177/D:269 ISOLDE: started sim > isolde pepflip /D:269 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 3 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /D:269 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /D:53/E:93 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 3 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /B:53/C:93 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /C:53/D:93 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /A:53/B:93 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /A:93/E:53 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 3 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /A:169/B:194 ISOLDE: started sim > volume #2.1.1.1 level 0.1876 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /A:169/B:194 ISOLDE: started sim > close #2.2.9 Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest bonded heavy atom. > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:169/C:194 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /A:194/E:169 ISOLDE: started sim Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest bonded heavy atom. > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:194 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /D:169/E:194 ISOLDE: started sim Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest bonded heavy atom. > volume #2.1.1.1 level 0.1895 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > save ""/Users/jessicakleiz/Library/Mobile > Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data > collection_CryoARM_VIB_SsCl > pH6.5/Doppio/job26/edited_ISOLDE/refined_expanded_ISOLDE-1.pdb"" > isolde sim start /C:169/D:194 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /A:243/E:237 ISOLDE: started sim > volume #2.1.1.1 level 0.1704 > volume #2.1.1.1 level 0.15 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /B:237/C:243 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /A:25/E:8 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 3 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /C:8/D:25 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 3 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /D:8/E:25 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /B:8/C:25 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /A:8/B:25 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 3 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /C:262/D:261 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:262/B:261 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:197 ISOLDE: started sim > isolde pepflip /A:197 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:197 ISOLDE: started sim > isolde pepflip /A:196 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:197 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:196 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /C:158 ISOLDE: started sim > isolde pepflip /C:158 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:152 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:149-155 ISOLDE: started sim > isolde pepflip /B:153 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /D:152 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:196 ISOLDE: started sim > isolde pepflip /B:197 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:197 ISOLDE: started sim > isolde pepflip /B:197 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:266 ISOLDE: started sim > isolde pepflip /B:266 > isolde pepflip #!2.2/B:266 > isolde stepto next > isolde stepto prev > isolde stepto next > isolde pepflip /B:267 > isolde stepto prev > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /B:266 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > volume #2.1.1.1 level 0.09923 > isolde sim start /B:197 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:197 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:42-43 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 3 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /B:9,71 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /A:93/E:53 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /C:53/D:93 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /A:324,328 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:42-43 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /C:48 ISOLDE: started sim > isolde pepflip /C:48 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 4 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /E:152 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:266 ISOLDE: started sim > isolde pepflip /A:266 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /D:236 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /C:152 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:152 ISOLDE: started sim > isolde pepflip /A:153 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:249 ISOLDE: started sim > isolde pepflip /A:249 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde pepflip /A:248 ISOLDE: started sim > isolde pepflip /A:248 > isolde pepflip /A:249 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:249 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /A:98 ISOLDE: started sim > isolde pepflip /A:98 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /C:98 ISOLDE: started sim > isolde pepflip /C:98 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /D:98 ISOLDE: started sim > isolde pepflip /D:98 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /D:142 ISOLDE: started sim > isolde pepflip /D:142 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /E:98 ISOLDE: started sim > isolde pepflip /E:98 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:98 ISOLDE: started sim > isolde pepflip /B:98 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /E:142 ISOLDE: started sim > isolde pepflip /E:142 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > save ""/Users/jessicakleiz/Library/Mobile > Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data > collection_CryoARM_VIB_SsCl > pH6.5/Doppio/job26/edited_ISOLDE/refined_expanded_ISOLDE-2.pdb"" > isolde sim start /B:142 ISOLDE: started sim > isolde pepflip /B:142 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /C:142 ISOLDE: started sim > isolde pepflip /C:142 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /A:142 ISOLDE: started sim > isolde pepflip /A:142 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /A:142 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /A:48 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /E:48 ISOLDE: started sim > isolde pepflip /E:48 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /D:266 ISOLDE: started sim > isolde pepflip /D:266 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /C:47-48 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > save ""/Users/jessicakleiz/Library/Mobile > Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data > collection_CryoARM_VIB_SsCl > pH6.5/Doppio/job26/edited_ISOLDE/refined_expanded_ISOLDE-3.pdb"" > select 5 Expected an objects specifier or a keyword > select 5 Expected an objects specifier or a keyword > select residues 5 Invalid ""residues"" argument: Expected true or false (or 1 or 0) > select resiue 5 Expected an objects specifier or a keyword > ui tool show ""Ramachandran Plot"" > isolde sim start /A:239 ISOLDE: started sim > isolde pepflip /A:239 > volume #2.1.1.1 level 0.134 > isolde pepflip /A:239 > isolde pepflip /A:240 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 3 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /A:239 ISOLDE: started sim > isolde pepflip /A:239 > isolde cisflip /A:239 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /A:239 ISOLDE: started sim > isolde sim pause > isolde sim resume > isolde sim pause > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /C:239 ISOLDE: started sim > isolde pepflip /C:239 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /D:239 ISOLDE: started sim > isolde pepflip /D:239 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /D:239 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /E:239 ISOLDE: started sim > isolde pepflip /E:239 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde pepflip /E:239 ISOLDE: started sim > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:239 ISOLDE: started sim > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:236-242 ISOLDE: started sim > isolde pepflip /B:239 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > volume #2.1.1.1 level 0.1497 > isolde sim start /B:239 ISOLDE: started sim > isolde pepflip /B:238 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > save ""/Users/jessicakleiz/Library/Mobile > Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data > collection_CryoARM_VIB_SsCl > pH6.5/Doppio/job26/edited_ISOLDE/refined_expanded_ISOLDE-4.pdb"" > isolde sim start /A:239 ISOLDE: started sim > isolde pepflip /A:239 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start #!2.2/A:239 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /A:5 ISOLDE: started sim > isolde pepflip /A:5 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /B:5 ISOLDE: started sim > isolde pepflip /B:5 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /C:5 ISOLDE: started sim > isolde pepflip /C:5 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /E:5 ISOLDE: started sim > isolde pepflip /E:5 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /D:5 ISOLDE: started sim > isolde pepflip /D:5 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > save ""/Users/jessicakleiz/Library/Mobile > Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data > collection_CryoARM_VIB_SsCl > pH6.5/Doppio/job26/edited_ISOLDE/refined_expanded_ISOLDE-5.pdb"" > isolde sim start /D:266 ISOLDE: started sim > isolde pepflip /D:266 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start /B:215/C:269 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start /A:269/E:215 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > save ""/Users/jessicakleiz/Library/Mobile > Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data > collection_CryoARM_VIB_SsCl > pH6.5/Doppio/job26/edited_ISOLDE/refined_expanded_ISOLDE-6.pdb"" ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/jessicakleiz/Library/Mobile > Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data > collection_CryoARM_VIB_SsCl > pH6.5/Doppio/job37_Gemmi_inputjob34/refined_gemmi_processed.cif- > coot-0_piece_cut.pdb"" Chain information for refined_gemmi_processed.cif-coot-0_piece_cut.pdb #1 --- Chain | Description A | No description available Computing secondary structure > set bgColor white > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > color #1 #0433ffff > color #1 #2b772cff > open ""/Users/jessicakleiz/Library/Mobile > Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data > collection_CryoARM_VIB_SsCl > pH6.5/Map/CS_Jobs/J29/J29_004_volume_map_sharp.mrc"" Opened J29_004_volume_map_sharp.mrc as #2, grid size 256,256,256, pixel 0.731, shown at level 0.216, step 1, values float32 > volume #2 level 0.1638 > transparency 50 > volume #2 level 0.132 > volume #2 level 0.1559 > isolde start > set selectionWidth 4 Done loading forcefield > isolde set simFidelityMode Medium/Medium ISOLDE: setting sim fidelity mode to Medium/Medium nonbonded_cutoff_distance = 0.900000 use_gbsa = True gbsa_cutoff = 1.100000 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 2 residues in model #1 to IUPAC-IUB standards. Chain information for refined_gemmi_processed.cif-coot-0_piece_cut.pdb --- Chain | Description 1.2/A | No description available ISOLDE: created disulfide bonds between the following residues: A131-A145; A69-A115 > clipper associate #2 toModel #1 Opened J29_004_volume_map_sharp.mrc as #1.1.1.1, grid size 256,256,256, pixel 0.731, shown at step 1, values float32 > volume style surface > transparency 50 > volume #1.1.1.1 color #2b772c > volume #1.1.1.1 color #2b772c2a > volume #1.1.1.1 level 0.2123 > volume #1.1.1.1 color #2b772c63 > select add #1.2 2725 atoms, 2798 bonds, 1 pseudobond, 324 residues, 10 models selected > select add #1.2 2725 atoms, 2798 bonds, 1 pseudobond, 324 residues, 10 models selected > ui tool show ""Ramachandran Plot"" OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M1 Max OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,4 Model Number: Z15G0040EFN/A Chip: Apple M1 Max Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 64 GB System Firmware Version: 11881.41.5 OS Loader Version: 11881.41.5 Software: System Software Overview: System Version: macOS 15.1.1 (24B91) Kernel Version: Darwin 24.1.0 Time since boot: 15 days, 29 minutes Graphics/Displays: Apple M1 Max: Chipset Model: Apple M1 Max Type: GPU Bus: Built-In Total Number of Cores: 24 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal LG HDR 4K: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 autocommand: 2.2.2 babel: 2.16.0 backports.tarfile: 1.2.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-Clipper: 0.24.0 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ISOLDE: 1.9 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 importlib_metadata: 8.0.0 importlib_resources: 6.4.0 inflect: 7.3.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jaraco.context: 5.3.0 jaraco.functools: 4.0.1 jaraco.text: 3.12.1 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 more-itertools: 10.3.0 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 ordered-set: 4.1.0 packaging: 23.2 packaging: 24.1 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 platformdirs: 4.2.2 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4.2 traitlets: 5.14.3 typeguard: 4.3.0 typing_extensions: 4.12.2 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 zipp: 3.19.2 }}} " defect assigned normal Window Toolkit all ChimeraX