id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4721 tilted slab: 'numpy.ndarray' object is not callable chimerax-bug-report@… Tristan Croll "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.2.4 (2021-05-14 07:23:00 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.2.4 (2021-05-14) © 2016-2021 Regents of the University of California. All rights reserved. > open ""/Users/liamgregory/iCloud Drive > (Archive)/Documents/UBC/crystals/20210409APS/Refine_54/comparison to NgPBP2 > working.cxs"" Unable to restore ""HKL_data_F_phi_float"" object restore_snapshot for ""XmapHandler_Static"" returned None restore_snapshot for ""FastVolumeSurface"" returned None restore_snapshot for ""FastVolumeSurface"" returned None Unable to restore ""HKL_data_F_phi_float"" object restore_snapshot for ""XmapHandler_Static"" returned None restore_snapshot for ""FastVolumeSurface"" returned None Unable to restore ""HKL_data_F_phi_float"" object restore_snapshot for ""XmapHandler_Static"" returned None restore_snapshot for ""FastVolumeSurface"" returned None Unable to restore ""HKL_data_F_phi_float"" object restore_snapshot for ""XmapHandler_Static"" returned None restore_snapshot for ""FastVolumeSurface"" returned None restore_snapshot for ""FastVolumeSurface"" returned None restore_snapshot for ""VolumeImage"" returned None restore_snapshot for ""VolumeImage"" returned None restore_snapshot for ""VolumeImage"" returned None restore_snapshot for ""VolumeImage"" returned None Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 1,1,1, pixel 0.62,0.62,0.598, shown at level -0.11, step 1, values float32 Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 1,1,1, pixel 0.62,0.62,0.598, shown at step 1, values float32 Opened (LIVE) 2mFo-DFc_sharp_2 as #1.1.1.4, grid size 1,1,1, pixel 0.62,0.62,0.598, shown at step 1, values float32 restore_snapshot for ""Redust"" returned None restore_snapshot for ""Redust"" returned None restore_snapshot for ""Redust"" returned None restore_snapshot for ""Redust"" returned None restore_snapshot for ""Redust"" returned None restore_snapshot for ""Redust"" returned None Log from Tue Jun 1 18:12:32 2021UCSF ChimeraX version: 1.2.4 (2021-05-14) © 2016-2021 Regents of the University of California. All rights reserved. > open ""/Users/liamgregory/iCloud Drive > (Archive)/Documents/UBC/crystals/20210409APS/Refine_54/consered resisdues > coloured.cxs"" Log from Tue Jun 1 16:43:26 2021UCSF ChimeraX version: 1.2.4 (2021-05-14) © 2016-2021 Regents of the University of California. All rights reserved. > open ""/Users/liamgregory/iCloud Drive > (Archive)/Documents/UBC/crystals/20210409APS/Refine_54/consered > resisdues.cxs"" Log from Tue Jun 1 16:27:29 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 > open ""/Users/liamgregory/iCloud Drive > (Archive)/Documents/UBC/crystals/20210409APS/Refine_54/spoVD_wt-5_refine_54.pdb"" Chain information for spoVD_wt-5_refine_54.pdb #1 --- Chain | Description A | No description available > select coil 1559 atoms, 1554 bonds, 4 pseudobonds, 219 residues, 2 models selected > ui tool show ""Color Actions"" > color sel medium sea green > select helix 1299 atoms, 1307 bonds, 172 residues, 1 model selected > ui tool show ""Color Actions"" > color sel cornflower blue > select strand 648 atoms, 637 bonds, 88 residues, 1 model selected > ui tool show ""Color Actions"" > color sel pink > select clear > select coil 1559 atoms, 1554 bonds, 4 pseudobonds, 219 residues, 2 models selected > ui tool show ""Color Actions"" > color sel light green > color sel pale green > select clear > ui mousemode right select > select /A:355@CG 1 atom, 1 residue, 1 model selected > select /A:355 10 atoms, 10 bonds, 1 residue, 1 model selected > select /A:3@ZN 1 atom, 1 residue, 1 model selected > select add /A:355@CB 2 atoms, 2 residues, 1 model selected > select /A:355 10 atoms, 10 bonds, 1 residue, 1 model selected > select add /A:3@ZN 11 atoms, 10 bonds, 2 residues, 1 model selected > select add /A:368 17 atoms, 15 bonds, 3 residues, 1 model selected > select add /A:348 23 atoms, 20 bonds, 4 residues, 1 model selected > select add /A:335 29 atoms, 25 bonds, 5 residues, 1 model selected > color sel byelement > ui mousemode right select > select ~sel 3504 atoms, 3551 bonds, 4 pseudobonds, 498 residues, 2 models selected > select clear > save ""/Users/liamgregory/iCloud Drive > (Archive)/Documents/UBC/crystals/20210409APS/Refine_54/secondary structure > colour.cxs"" > select clear > select clear > ui mousemode right translate > ui mousemode right select > select /B:2@CO 1 atom, 1 residue, 1 model selected > select /B:1@CO 1 atom, 1 residue, 1 model selected > select add /B:2@CO 2 atoms, 2 residues, 1 model selected > select ligand 4 atoms, 3 bonds, 1 residue, 1 model selected > select clear > ui mousemode right select > select /B:2@CO 1 atom, 1 residue, 1 model selected > select /B:1@CO 1 atom, 1 residue, 1 model selected > select add /B:2@CO 2 atoms, 2 residues, 1 model selected > color sel byhetero > color sel red > color sel byelement > select clear > select clear > ui mousemode right translate > select sequence ""311, 314,367,369,512,513,514,515"" Nothing selected > select sequence 311 Nothing selected > select clearselect /B:311,314,367,369,512-515 Expected an objects specifier or a keyword > select /B:311,314,367,369,512-515 Nothing selected > select :311,314,367,369,512-515 56 atoms, 51 bonds, 8 residues, 1 model selected > style sel stick Changed 56 atom styles > style sel stick Changed 56 atom styles > show sel atoms > color sel byhetero > select clear > select :426 4 atoms, 3 bonds, 1 residue, 1 model selected > ui mousemode right select > ui mousemode right distance > ui mousemode right distance > ui mousemode right select > ui mousemode right distance > ui mousemode right distance > distance :267 :513 Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got 14 > distance :267@o :513@o Distance between /A PRO 267 O and THR 513 O: 35.839Å > distance :367@o :513@o Distance between /A SER 367 O and THR 513 O: 8.915Å > distance :367@oc :513@oc Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got 0 > distance :367@ob :513@oc Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got 0 > distance :367@og :513@og1 Distance between /A SER 367 OG and THR 513 OG1: 6.146Å > ui mousemode right translate > distance :311@og :515@n Distance between /A SER 311 OG and THR 515 N: 2.935Å > clear labels Unknown command: clear labels > labels clear Unknown command: labels clear > label clear Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword > hide #2.1 models > hide #!2 models > select clear > select :426 4 atoms, 3 bonds, 1 residue, 1 model selected > save ""/Users/liamgregory/iCloud Drive > (Archive)/Documents/UBC/crystals/20210409APS/Refine_54/consered > resisdues.cxs"" ——— End of log from Tue Jun 1 16:27:29 2021 ——— opened ChimeraX session > select :311,314,367,369,512-515,426,355,335,348,368 88 atoms, 81 bonds, 3 pseudobonds, 13 residues, 2 models selected > select ~sel 3445 atoms, 3495 bonds, 9 pseudobonds, 490 residues, 5 models selected > color (#!1 & sel) light gray > undo > undo > redo > ui mousemode right select > select /A:3@ZN 1 atom, 1 residue, 1 model selected > undo > select subtract /A:3@ZN 3444 atoms, 3495 bonds, 9 pseudobonds, 489 residues, 5 models selected > select subtract /B:2@CO 3443 atoms, 3495 bonds, 9 pseudobonds, 488 residues, 5 models selected > select subtract /B:1@CO 3442 atoms, 3495 bonds, 9 pseudobonds, 487 residues, 5 models selected > ui tool show ""Color Actions"" > color sel light steel blue > select clear Drag select of 2 residues Drag select of 4 residues > select clear Drag select of 2 residues > select clear > select :311,314 15 atoms, 13 bonds, 2 residues, 1 model selected > ui tool show ""Color Actions"" > color sel dark violet > select :367,369 14 atoms, 12 bonds, 2 residues, 1 model selected > color sel orange > select :512-515 27 atoms, 26 bonds, 4 residues, 1 model selected > color sel cyan > select :426 4 atoms, 3 bonds, 1 residue, 1 model selected > color sel forest green > select :311,314,367,369,512-515,426 60 atoms, 54 bonds, 3 pseudobonds, 9 residues, 2 models selected > color (#!1 & sel) byhetero > select clear > ui mousemode right translate > ui mousemode right select > select add /A:368 6 atoms, 5 bonds, 1 residue, 1 model selected > select add /A:348 12 atoms, 10 bonds, 2 residues, 1 model selected > select add /A:335 18 atoms, 15 bonds, 3 residues, 1 model selected > select add /A:355 28 atoms, 25 bonds, 4 residues, 1 model selected > select clear > select add /A:335 6 atoms, 5 bonds, 1 residue, 1 model selected > select add /A:355 16 atoms, 15 bonds, 2 residues, 1 model selected > select add /A:368 22 atoms, 20 bonds, 3 residues, 1 model selected > select add /A:348 28 atoms, 25 bonds, 4 residues, 1 model selected > color sel dark gray > color sel byhetero > select clear > select :335,348,355,368 28 atoms, 25 bonds, 4 residues, 1 model selected > color sel dim gray > color sel gray > color sel dark gray > color sel light gray > color sel dim gray > color sel gray > select clear > color sel light gray > ui tool show ""Color Actions"" > color sel slate gray > color sel light slate gray > color sel dim gray > color sel gray > color sel silver > color sel light gray > color sel silver > color sel light steel blue > color sel byhetero > select clear Drag select of 3 residues > select clear > ui mousemode right zoom > ui mousemode right translate > save ""/Users/liamgregory/iCloud Drive > (Archive)/Documents/UBC/crystals/20210409APS/Refine_54/consered resisdues > coloured.cxs"" ——— End of log from Tue Jun 1 16:43:26 2021 ——— opened ChimeraX session > mmaker > matchmaker Missing or invalid ""matchAtoms"" argument: empty atom specifier > toolshed show > ui tool show Matchmaker > open /Users/liamgregory/Desktop/3equ.pdb 3equ.pdb title: Crystal structure of penicillin-binding protein 2 from neisseria gonorrhoeae [more info...] Chain information for 3equ.pdb #3 --- Chain | Description A B | PBP-2 Non-standard residues in 3equ.pdb #3 --- GOL — glycerol (glycerin; propane-1,2,3-triol) SO4 — sulfate ion > matchmaker #!3 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker spoVD_wt-5_refine_54.pdb, chain A (#1) with 3equ.pdb, chain A (#3), sequence alignment score = 731.3 RMSD between 305 pruned atom pairs is 0.962 angstroms; (across all 373 pairs: 3.330) > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!1 models > select :310,313,362,364,497-500,421 156 atoms, 140 bonds, 23 residues, 2 models selected > select :310,313,362,364,497-500,421 #3 6795 atoms, 6749 bonds, 5 pseudobonds, 1025 residues, 3 models selected > select #3:310,313,362,364,497-500,421 120 atoms, 108 bonds, 18 residues, 1 model selected > show sel atoms > select ~sel 10172 atoms, 10185 bonds, 17 pseudobonds, 1505 residues, 7 models selected > hide sel & #!3 cartoons > hide sel & #!3 cartoons > style sel & #!3 stick Changed 6639 atom styles > hide sel & #!3 atoms > select ~sel 120 atoms, 108 bonds, 18 residues, 1 model selected > ui tool show ""Color Actions"" > color sel orchid > color sel byhetero > show #!1 models > hide #!1 models > select clear > select #1 3533 atoms, 3576 bonds, 12 pseudobonds, 503 residues, 4 models selected > show #!1 models > show sel cartoons > show sel cartoons > select #3 6759 atoms, 6717 bonds, 5 pseudobonds, 1020 residues, 2 models selected > select #3 6759 atoms, 6717 bonds, 5 pseudobonds, 1020 residues, 2 models selected > hide sel cartoons > undo > select #1:311,314,367,369,512-515,426 60 atoms, 54 bonds, 3 pseudobonds, 9 residues, 2 models selected > ui tool show ""Color Actions"" > color sel light steel blue > select clear > select #1:311,314,367,369,512-515,426 60 atoms, 54 bonds, 3 pseudobonds, 9 residues, 2 models selected > color (#!1 & sel) byhetero > select #3:310,313,362,364,497-500,421 120 atoms, 108 bonds, 18 residues, 1 model selected > select clear > select #3:310,313,362,364,497-500,421 120 atoms, 108 bonds, 18 residues, 1 model selected > select #1:311,314,367,369,512-515,426 60 atoms, 54 bonds, 3 pseudobonds, 9 residues, 2 models selected > color (#!1 & sel) cyan > color (#!1 & sel) byhetero > select clear > open ""/Users/liamgregory/iCloud Drive > (Archive)/Documents/UBC/crystals/20210409APS/Refine_54/spoVD_wt-5_refine_54.mtz"" > structureModel Missing ""structureModel"" keyword's argument > open ""/Users/liamgregory/iCloud Drive > (Archive)/Documents/UBC/crystals/20210409APS/Refine_54/spoVD_wt-5_refine_54.mtz"" > structureModel #1 Summary of feedback from opening /Users/liamgregory/iCloud Drive (Archive)/Documents/UBC/crystals/20210409APS/Refine_54/spoVD_wt-5_refine_54.mtz --- warning | WARNING: multiple experimental reflection datasets found: (Original-experimental-data-mapped-to-asu) I-obs, SIGI-obs, (Experimental-data-used-in-refinement) F-obs-filtered, SIGF-obs-filtered Automatically choosing ""(Experimental-data-used-in-refinement) F-obs-filtered, SIGF-obs-filtered"". Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 64,46,42, pixel 0.62,0.62,0.598, shown at level 0.231, step 1, values float32 Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 64,46,42, pixel 0.62,0.62,0.598, shown at level -0.0722,0.0722, step 1, values float32 Opened (LIVE) 2mFo-DFc_sharp_2 as #1.1.1.4, grid size 64,46,42, pixel 0.62,0.62,0.598, shown at level 0.325, step 1, values float32 Opened (STATIC) (Model-structure-factors-(bulk-solvent-and-all-scales- included)) F-model, PHIF-model as #1.1.1.5, grid size 64,46,42, pixel 0.62,0.62,0.598, shown at level -0.335,0.335, step 1, values float32 Opened (STATIC) (Fourier-map-coefficients) 2FOFCWT, PH2FOFCWT as #1.1.1.6, grid size 64,46,42, pixel 0.62,0.62,0.598, shown at level 0.243, step 1, values float32 Opened (STATIC) (Fourier-map-coefficients) 2FOFCWT_no_fill, PH2FOFCWT_no_fill as #1.1.1.7, grid size 64,46,42, pixel 0.62,0.62,0.598, shown at level 0.233, step 1, values float32 Opened (STATIC) (Fourier-map-coefficients) FOFCWT, PHFOFCWT as #1.1.1.8, grid size 64,46,42, pixel 0.62,0.62,0.598, shown at level -0.149,0.149, step 1, values float32 Opened crystallographic dataset from /Users/liamgregory/iCloud Drive (Archive)/Documents/UBC/crystals/20210409APS/Refine_54/spoVD_wt-5_refine_54.mtz Found experimental reflection data: (Experimental-data-used-in-refinement) F-obs-filtered, SIGF-obs-filtered Rwork: 0.2339; Rfree: 0.2841 Generated maps: Reflection Data (LIVE) 2mFo-DFc (LIVE) mFo-DFc (LIVE) 2mFo-DFc_sharp_2 (STATIC) (Model-structure-factors-(bulk-solvent-and-all-scales-included)) F-model, PHIF-model (STATIC) (Fourier-map-coefficients) 2FOFCWT, PH2FOFCWT (STATIC) (Fourier-map-coefficients) 2FOFCWT_no_fill, PH2FOFCWT_no_fill (STATIC) (Fourier-map-coefficients) FOFCWT, PHFOFCWT Any unwanted maps may be safely closed via the Model panel. > hide #1.3 models > hide #!1.2 models > show #!1.2 models > undo > undo > undo > undo > undo > undo > undo > undo > redo > hide #1.3 models > show #1.3 models > hide #1.3 models > show #1.3 models > hide #1.3 models > show #1.3 models > hide #!1.1 models > show #!1.1 models > hide #!1.1 models > select ~sel 10232 atoms, 10239 bonds, 14 pseudobonds, 1514 residues, 37 models selected > hide sel atoms > show sel atoms > hide sel atoms > undo > undo > undo > undo > undo > redo > redo > undo > undo > hide #1.3 models > show #1.3 models > hide #1.3 models > show #1.3 models > hide #1.3 models > show #1.3 models > hide #1.3 models > show #1.3 models > select #1.3 1 model selected > select #1.3 1 model selected > select #1.3 1 model selected > select #3 6759 atoms, 6717 bonds, 5 pseudobonds, 1020 residues, 2 models selected > hide #1.3 models > select #1:311,314,367,369,512-515,426 60 atoms, 54 bonds, 3 pseudobonds, 9 residues, 2 models selected > select #1:311,314,367,369,512-515,426 60 atoms, 54 bonds, 3 pseudobonds, 9 residues, 2 models selected > select #1:311,314,367,369,512-515,426select #3:310,313,362,364,497-500,421 176 atoms, 159 bonds, 3 pseudobonds, 26 residues, 3 models selected > select ~sel 10116 atoms, 10134 bonds, 14 pseudobonds, 1497 residues, 37 models selected > hide sel atoms > ~select Nothing selected > transparency 0 > volume style image > volume style image > volume style mesh > volume style surface > volume style image > volume style mesh > volume showOutlineBox true > volume step 1 > volume step 2 > hide #!1.1.1 models > show #!1.1.1 models > hide #!1.1.1 models > show #!1.1.1 models > hide #1.2.2 models > surface dust #1.1.1.2 size 6.2 > surface dust #1.1.1.3 size 6.2 > surface dust #1.1.1.4 size 6.2 > surface dust #1.1.1.5 size 6.2 > surface dust #1.1.1.6 size 6.2 > surface dust #1.1.1.7 size 6.2 > surface dust #1.1.1.8 size 6.2 > undo Color zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic models, 7 maps. Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 2 atomic models, 7 maps. > transparency 50 > hide #!1.1.1.1 models > show #!1.1.1.1 models > hide #!1.1.1.2 models > show #!1.1.1.2 models > hide #!1.1.1.2 models > show #!1.1.1.2 models > hide #!1.1.1.3 models > show #!1.1.1.3 models > hide #!1.1.1.3 models > hide #!1.1.1.2 models > hide #!1.1.1.8 models > hide #!1.1.1.7 models > show #!1.1.1.7 models > hide #!1.1.1.7 models > hide #!1.1.1.6 models > hide #!1.1.1.5 models > hide #!1.1.1.4 models > show #!1.1.1.2 models > show #1.1.1.2.2 models > hide #1.1.1.2.2 models > show #1.1.1.2.2 models > hide #1.1.1.2.2 models > volume #!1.1.1.2 step 2 > volume #!1.1.1.2 step 2 > volume #!1.1.1.2 step 2 > volume #!1.1.1.2 step 1 > volume #!1.1.1.2 step 1 > volume #!1.1.1.2 step 2 > volume #!1.1.1.2 step 1 > volume #!1.1.1.2 step 2 > volume #!1.1.1.2 style mesh > volume #!1.1.1.2 showOutlineBox false Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 2 atomic models, 1 maps. > show #1.1.1.2.2 models > hide #1.1.1.2.1 models > show #1.1.1.2.1 models > volume #!1.1.1.2 showOutlineBox true > volume #!1.1.1.2 showOutlineBox false > transparency #1.1.1.2.1 50 > transparency #1.1.1.2.1 0 > volume #!1.1.1.2 planes z style image imageMode ""full region"" > mousemode rightMode ""move planes"" > volume #1.1.1.2 style image region all imageMode ""tilted slab"" > tiltedSlabAxis 0,0,1 tiltedSlabOffset 23.93 tiltedSlabSpacing 0.5982 > tiltedSlabPlaneCount 10 > mousemode rightMode ""rotate slab"" > volume #1.1.1.3 style image region all imageMode ""tilted slab"" > tiltedSlabAxis 0,0,1 tiltedSlabOffset 23.93 tiltedSlabSpacing 0.5982 > tiltedSlabPlaneCount 10 > mousemode rightMode ""rotate slab"" > volume #1.1.1.4 style image region all imageMode ""tilted slab"" > tiltedSlabAxis 0,0,1 tiltedSlabOffset 23.93 tiltedSlabSpacing 0.5982 > tiltedSlabPlaneCount 10 > mousemode rightMode ""rotate slab"" > volume #1.1.1.5 style image region all imageMode ""tilted slab"" > tiltedSlabAxis 0,0,1 tiltedSlabOffset 23.93 tiltedSlabSpacing 0.5982 > tiltedSlabPlaneCount 10 > mousemode rightMode ""rotate slab"" > volume #1.1.1.6 style image region all imageMode ""tilted slab"" > tiltedSlabAxis 0,0,1 tiltedSlabOffset 23.93 tiltedSlabSpacing 0.5982 > tiltedSlabPlaneCount 10 > mousemode rightMode ""rotate slab"" > volume #1.1.1.7 style image region all imageMode ""tilted slab"" > tiltedSlabAxis 0,0,1 tiltedSlabOffset 23.93 tiltedSlabSpacing 0.5982 > tiltedSlabPlaneCount 10 > mousemode rightMode ""rotate slab"" > volume #1.1.1.8 style image region all imageMode ""tilted slab"" > tiltedSlabAxis 0,0,1 tiltedSlabOffset 23.93 tiltedSlabSpacing 0.5982 > tiltedSlabPlaneCount 10 > mousemode rightMode ""rotate slab"" > volume #1.1.1.2 orthoplanes xyz positionPlanes 32,23,21 style image region > all > mousemode rightMode ""move planes"" > volume #1.1.1.3 orthoplanes xyz positionPlanes 32,23,21 style image region > all > mousemode rightMode ""move planes"" > volume #1.1.1.4 orthoplanes xyz positionPlanes 32,23,21 style image region > all > mousemode rightMode ""move planes"" > volume #1.1.1.5 orthoplanes xyz positionPlanes 32,23,21 style image region > all > mousemode rightMode ""move planes"" > volume #1.1.1.6 orthoplanes xyz positionPlanes 32,23,21 style image region > all > mousemode rightMode ""move planes"" > volume #1.1.1.7 orthoplanes xyz positionPlanes 32,23,21 style image region > all > mousemode rightMode ""move planes"" > volume #1.1.1.8 orthoplanes xyz positionPlanes 32,23,21 style image region > all > mousemode rightMode ""move planes"" > volume #!1.1.1.2 region all imageMode ""full region"" > volume unzone #!1.1.1.2 > mousemode rightMode ""crop volume"" Volume zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic models, 1 maps. > volume #!1.1.1.2 style mesh > volume #!1.1.1.2 style image > volume #!1.1.1.2 style mesh > hide #!1.1.1.1 models > show #!1.1.1.1 models > hide #!1.1.1.1 models > hide #!1.1.1.2 models > show #!1.1.1.2 models > hide #1.1.1.2.1 models > show #1.1.1.2.1 models > hide #!1.1.1 models > show #!1.1.1 models > show #!1.1.1.5 models > hide #!1.1.1.5 models > show #!1.1.1.6 models > hide #!1.1.1.6 models > show #!1.1.1.7 models > hide #!1.1.1.7 models > show #!1.1.1.6 models > volume #!1.1.1.2,6 style mesh > hide #!1.1.1.6 models > volume #1.1.1.2 region 0,0,0,63,45,41 > rmslevel 1 Unknown command: rmslevel 1 > ui tool show ""Volume Viewer"" > volume #1.1.1.2 change image level -0.1666,0 level 0.44,0.8 level 1.148,1 > volume #1.1.1.2 level 0.1517 > volume #1.1.1.2 region 0,0,0,63,45,41 > volume #1.1.1.2 region 0,0,0,63,45,41 > volume #1.1.1.2 region 0,0,0,63,45,28 > volume #1.1.1.2 region 0,0,0,63,45,29 > volume #1.1.1.2 level 0.1052 > volume #1.1.1.2 level 0.1597 > volume #1.1.1.2 level 0.07095 > volume #1.1.1.2 region 0,0,0,63,31,29 > volume #1.1.1.2 region 0,0,0,63,31,29 > volume #1.1.1.2 region 0,0,0,63,39,29 > volume #1.1.1.2 region 0,0,0,63,39,28 > volume #1.1.1.2 level -0.1101 > ui tool show ""Hide Dust"" > surface dust #1.1.1.2 size 1.85 > surface dust #1.1.1.2 size 1.85 > surface undust #1.1.1.2 > surface dust #1.1.1.2 size 1.85 > save ""/Users/liamgregory/iCloud Drive > (Archive)/Documents/UBC/crystals/20210409APS/Refine_54/comparison to NgPBP2 > working.cxs"" includeMaps true Unable to save '_surface_updaters' -> -> -> 'surface' -> '(STATIC) (Fourier-map-coefficients) 2FOFCWT_no_fill, PH2FOFCWT_no_fill' -> "". Session might not restore properly. Unable to save '_surface_updaters' -> -> -> 'surface' -> '(STATIC) (Model-structure-factors-(bulk-solvent- and-all-scales-included)) F-model, PHIF-model' -> "". Session might not restore properly. Unable to save '_surface_updaters' -> -> -> 'surface' -> '(STATIC) (Fourier-map-coefficients) FOFCWT, PHFOFCWT' -> "". Session might not restore properly. Unable to save '_surface_updaters' -> -> -> 'surface' -> '(STATIC) (Fourier-map-coefficients) 2FOFCWT, PH2FOFCWT' -> "". Session might not restore properly. ——— End of log from Tue Jun 1 18:12:32 2021 ——— opened ChimeraX session > hide #1.3 models > show #1.3 models > hide #1.3 models > show #1.3 models > hide #1.3 models > hide #!1.2 models > show #!1.2 models > hide #!1.2 models > show #!1.2 models > hide #1.2.2 models > show #1.2.2 models > hide #1.2.2 models > hide #1.1.1.2.1 models > show #1.1.1.2.1 models > select #1:311,314,367,369,512-515,426 60 atoms, 54 bonds, 3 pseudobonds, 9 residues, 2 models selected > select #1:311,314,367,369,512-515,426,#3 Expected an objects specifier or a keyword > select #1:311,314,367,369,512-515,426,#3 Expected an objects specifier or a keyword > select #1:311,314,367,369,512-515,426,#3: Expected an objects specifier or a keyword > select #3 6759 atoms, 6717 bonds, 5 pseudobonds, 1020 residues, 2 models selected > select #3,#1 Expected an objects specifier or a keyword > select add #3 6759 atoms, 6717 bonds, 5 pseudobonds, 1020 residues, 2 models selected > hide sel atoms > undo > select invert Expected an objects specifier or a keyword > select inv Expected an objects specifier or a keyword > select invert Expected an objects specifier or a keyword > select ~sel 3533 atoms, 3576 bonds, 12 pseudobonds, 503 residues, 28 models selected > hide sel atoms > hide sel cartoons > select clear > select clear > select #1 3533 atoms, 3576 bonds, 12 pseudobonds, 503 residues, 27 models selected > show sel cartoons > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > nucleotides sel fill > style nucleic & sel stick Changed 0 atom styles > nucleotides sel slab > style nucleic & sel stick Changed 0 atom styles > nucleotides sel tube/slab shape box > cartoon (#!1.2 & sel) > select clear > ui mousemode right ""contour level"" > volume #1.1.1.2 level -0.1621 > volume #1.1.1.2 level -0.1695 > ui mousemode right translate > select #1 3533 atoms, 3576 bonds, 12 pseudobonds, 503 residues, 27 models selected > 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 > select clear > volume #!1.1.1.2 step 2 > volume #!1.1.1.2 showOutlineBox false > volume #!1.1.1.2 style surface > volume #!1.1.1.2 step 1 > volume #!1.1.1.2 step 2 > vop gaussian #1.1.1.2 sdev 1.86 Opened (LIVE) 2mFo-DFc gaussian as #4, grid size 64,46,42, pixel 0.62,0.62,0.598, shown at step 1, values float32 > undo > undo > redo > redo Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 2 atomic models, 1 maps. > vop gaussian #4 sdev 1.86 Opened (LIVE) 2mFo-DFc gaussian as #5, grid size 64,46,42, pixel 0.62,0.62,0.598, shown at step 1, values float32 > vop gaussian #5 sdev 1.86 Opened (LIVE) 2mFo-DFc gaussian as #6, grid size 64,46,42, pixel 0.62,0.62,0.598, shown at step 1, values float32 > vop gaussian #6 sdev 1.86 Opened (LIVE) 2mFo-DFc gaussian as #7, grid size 64,46,42, pixel 0.62,0.62,0.598, shown at step 1, values float32 > vop gaussian #7 sdev 1.86 Opened (LIVE) 2mFo-DFc gaussian as #8, grid size 64,46,42, pixel 0.62,0.62,0.598, shown at step 1, values float32 > vop gaussian #8 sdev 1.86 Opened (LIVE) 2mFo-DFc gaussian as #9, grid size 64,46,42, pixel 0.62,0.62,0.598, shown at step 1, values float32 > vop gaussian #9 sdev 1.86 Opened (LIVE) 2mFo-DFc gaussian as #10, grid size 64,46,42, pixel 0.62,0.62,0.598, shown at step 1, values float32 > vop gaussian #10 sdev 1.86 Opened (LIVE) 2mFo-DFc gaussian as #11, grid size 64,46,42, pixel 0.62,0.62,0.598, shown at step 1, values float32 > undo > undo > undo > undo > undo > undo > redo > redo > redo > redo > redo > redo > volume #!11 style surface > volume #!11 style mesh > volume #!11 style surface > volume #!11 style mesh > volume #!11 style image > volume #!11 style mesh > volume #1.1.1.2 level -0.1837 > hide #!11 models > close #11 > show #!10 models > show #!9 models > show #!8 models > close #8 > close #4-7,9-10 > volume #!1.1.1.2 style mesh > volume #!1.1.1.2 step 2 > volume #!1.1.1.2 step 1 > select #1:311,314,367,369,512-515,426 60 atoms, 54 bonds, 3 pseudobonds, 9 residues, 2 models selected > show sel atoms > color (#!1.2 & sel) byhetero > ui mousemode right windowing > ui mousemode right ""contour level"" > volume #1.1.1.2 level -0.008835 > volume #1.1.1.2 level -0.1344 > volume #1.1.1.2 level -0.1909 > volume #1.1.1.2 level -0.1499 > volume #1.1.1.2 level -0.08227 > volume #1.1.1.2 level -0.2298 > volume #1.1.1.2 level -0.3325 > volume #1.1.1.2 level 0.0292 > volume #1.1.1.2 level -0.03678 > volume #1.1.1.2 level -0.06178 > volume #1.1.1.2 level -0.1603 > volume #1.1.1.2 level -0.2452 > hide #!3 models > volume #1.1.1.2 level -0.1876 > volume #1.1.1.2 level -0.3008 > volume #1.1.1.2 level -0.2474 > ui mousemode right ""move planes"" > volume #1.1.1.2 region 0,0,0,63,45,41 > volume #1.1.1.2 region 0,0,0,63,45,41 > volume #1.1.1.2 region 0,0,0,63,45,41 > ui mousemode right ""rotate slab"" Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 637, in gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_down"") File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 537, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 33, in mouse_down self._choose_map(line) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 46, in _choose_map self._set_initial_slab() File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 50, in _set_initial_slab set_initial_tilted_slab(self._map, matching_maps = self._matching_maps) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 192, in set_initial_tilted_slab offset = inner_product(axis, v.center()) TypeError: 'numpy.ndarray' object is not callable TypeError: 'numpy.ndarray' object is not callable File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 192, in set_initial_tilted_slab offset = inner_product(axis, v.center()) See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 638, in gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_drag"") File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 537, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 105, in mouse_drag self._rotate_slab(raxis, rangle) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 121, in _rotate_slab offset = soffset + inner_product(axis-saxis, rcenter) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 638, in gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_drag"") File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 537, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 105, in mouse_drag self._rotate_slab(raxis, rangle) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 121, in _rotate_slab offset = soffset + inner_product(axis-saxis, rcenter) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 638, in gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_drag"") File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 537, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 105, in mouse_drag self._rotate_slab(raxis, rangle) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 121, in _rotate_slab offset = soffset + inner_product(axis-saxis, rcenter) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 638, in gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_drag"") File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 537, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 105, in mouse_drag self._rotate_slab(raxis, rangle) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 121, in _rotate_slab offset = soffset + inner_product(axis-saxis, rcenter) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 638, in gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_drag"") File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 537, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 105, in mouse_drag self._rotate_slab(raxis, rangle) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 121, in _rotate_slab offset = soffset + inner_product(axis-saxis, rcenter) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 638, in gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_drag"") File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 537, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 105, in mouse_drag self._rotate_slab(raxis, rangle) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 121, in _rotate_slab offset = soffset + inner_product(axis-saxis, rcenter) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 638, in gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_drag"") File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 537, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 105, in mouse_drag self._rotate_slab(raxis, rangle) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 121, in _rotate_slab offset = soffset + inner_product(axis-saxis, rcenter) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 638, in gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_drag"") File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 537, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 105, in mouse_drag self._rotate_slab(raxis, rangle) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 121, in _rotate_slab offset = soffset + inner_product(axis-saxis, rcenter) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 638, in gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_drag"") File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 537, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 105, in mouse_drag self._rotate_slab(raxis, rangle) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 121, in _rotate_slab offset = soffset + inner_product(axis-saxis, rcenter) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 638, in gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_drag"") File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 537, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 105, in mouse_drag self._rotate_slab(raxis, rangle) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 121, in _rotate_slab offset = soffset + inner_product(axis-saxis, rcenter) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 638, in gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_drag"") File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 537, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 105, in mouse_drag self._rotate_slab(raxis, rangle) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 121, in _rotate_slab offset = soffset + inner_product(axis-saxis, rcenter) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 638, in gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_drag"") File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 537, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 105, in mouse_drag self._rotate_slab(raxis, rangle) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 121, in _rotate_slab offset = soffset + inner_product(axis-saxis, rcenter) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 638, in gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_drag"") File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 537, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 105, in mouse_drag self._rotate_slab(raxis, rangle) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 121, in _rotate_slab offset = soffset + inner_product(axis-saxis, rcenter) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 638, in gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_drag"") File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 537, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 105, in mouse_drag self._rotate_slab(raxis, rangle) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 121, in _rotate_slab offset = soffset + inner_product(axis-saxis, rcenter) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 638, in gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_drag"") File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 537, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 105, in mouse_drag self._rotate_slab(raxis, rangle) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 121, in _rotate_slab offset = soffset + inner_product(axis-saxis, rcenter) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 638, in gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_drag"") File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 537, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 105, in mouse_drag self._rotate_slab(raxis, rangle) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 121, in _rotate_slab offset = soffset + inner_product(axis-saxis, rcenter) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 638, in gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_drag"") File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 537, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 105, in mouse_drag self._rotate_slab(raxis, rangle) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 121, in _rotate_slab offset = soffset + inner_product(axis-saxis, rcenter) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 638, in gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_drag"") File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 537, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 105, in mouse_drag self._rotate_slab(raxis, rangle) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 121, in _rotate_slab offset = soffset + inner_product(axis-saxis, rcenter) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 638, in gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_drag"") File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 537, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 105, in mouse_drag self._rotate_slab(raxis, rangle) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 121, in _rotate_slab offset = soffset + inner_product(axis-saxis, rcenter) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 638, in gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_drag"") File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 537, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 105, in mouse_drag self._rotate_slab(raxis, rangle) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 121, in _rotate_slab offset = soffset + inner_product(axis-saxis, rcenter) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 638, in gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_drag"") File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 537, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 105, in mouse_drag self._rotate_slab(raxis, rangle) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 121, in _rotate_slab offset = soffset + inner_product(axis-saxis, rcenter) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 638, in gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_drag"") File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 537, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 105, in mouse_drag self._rotate_slab(raxis, rangle) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 121, in _rotate_slab offset = soffset + inner_product(axis-saxis, rcenter) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 638, in gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_drag"") File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 537, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 105, in mouse_drag self._rotate_slab(raxis, rangle) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 121, in _rotate_slab offset = soffset + inner_product(axis-saxis, rcenter) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 638, in gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_drag"") File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 537, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 105, in mouse_drag self._rotate_slab(raxis, rangle) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 121, in _rotate_slab offset = soffset + inner_product(axis-saxis, rcenter) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 638, in gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_drag"") File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 537, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 105, in mouse_drag self._rotate_slab(raxis, rangle) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 121, in _rotate_slab offset = soffset + inner_product(axis-saxis, rcenter) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 638, in gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_drag"") File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 537, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 105, in mouse_drag self._rotate_slab(raxis, rangle) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 121, in _rotate_slab offset = soffset + inner_product(axis-saxis, rcenter) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 638, in gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, ""mouse_drag"") File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/mouse_modes/mousemodes.py"", line 537, in _dispatch_mouse_event f(MouseEvent(event, modifiers=modifiers)) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 105, in mouse_drag self._rotate_slab(raxis, rangle) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/map/tiltedslab.py"", line 121, in _rotate_slab offset = soffset + inner_product(axis-saxis, rcenter) File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] TypeError: 'NoneType' object is not subscriptable TypeError: 'NoneType' object is not subscriptable File ""/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/geometry/vector.py"", line 58, in inner_product return u[0]*v[0] + u[1]*v[1] + u[2]*v[2] See log for complete Python traceback. > volume #1.1.1.2 tiltedSlabAxis 0,0,1 tiltedSlabOffset 23.93 OpenGL version: 4.1 INTEL-16.1.12 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655 OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro15,2 Processor Name: Quad-Core Intel Core i7 Processor Speed: 2.8 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 8 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1554.80.3.0.0 (iBridge: 18.16.14347.0.0,0) Software: System Software Overview: System Version: macOS 11.2.3 (20D91) Kernel Version: Darwin 20.3.0 Time since boot: 19 days 11:13 Graphics/Displays: Intel Iris Plus Graphics 655: Chipset Model: Intel Iris Plus Graphics 655 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3ea5 Revision ID: 0x0001 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal *22W1*: Resolution: 1680 x 1050 (Widescreen Super eXtended Graphics Array Plus) UI Looks like: 1680 x 1050 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: 80200805 Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: Yes Connection Type: Analog VGA or Analog Over DVI-I Adapter Firmware Version: 2.22 Locale: (None, 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.12.5 cftime: 1.4.1 chardet: 3.0.4 ChimeraX-AddCharge: 1.0 ChimeraX-AddH: 2.1.6 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.13.3 ChimeraX-AtomicLibrary: 3.1.3 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.5.2 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1 ChimeraX-Clipper: 0.16.1 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.2.1 ChimeraX-CommandLine: 1.1.4 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.2.4 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.1.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.3 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.0 ChimeraX-Hbonds: 2.1 ChimeraX-Help: 1.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.0.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.2.1 ChimeraX-MDcrds: 2.2 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.3 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.0.1 ChimeraX-ModelPanel: 1.0.1 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: 2.0.1 ChimeraX-OpenCommand: 1.5 ChimeraX-PDB: 2.4.1 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.1 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.0.1 ChimeraX-ReadPbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.4 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.3.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.0.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.7.4 ChimeraX-uniprot: 2.1 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.21 decorator: 5.0.7 distlib: 0.3.1 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.17 imagecodecs: 2020.5.30 imagesize: 1.2.0 ipykernel: 5.3.4 ipython: 7.18.1 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.7 jupyter-core: 4.7.1 kiwisolver: 1.3.1 line-profiler: 2.1.2 lxml: 4.6.2 lz4: 3.1.0 MarkupSafe: 2.0.0 matplotlib: 3.3.2 matplotlib-inline: 0.1.2 msgpack: 1.0.0 netCDF4: 1.5.4 networkx: 2.5 numexpr: 2.7.3 numpy: 1.19.2 numpydoc: 1.1.0 openvr: 1.14.1501 packaging: 20.9 ParmEd: 3.2.0 parso: 0.7.1 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 7.2.0 pip: 21.0.1 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.18 psutil: 5.7.2 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.7.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.1 pytz: 2021.1 pyzmq: 22.0.3 qtconsole: 4.7.7 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.5.2 setuptools: 50.3.2 sfftk-rw: 0.6.7.dev1 six: 1.15.0 snowballstemmer: 2.1.0 sortedcontainers: 2.2.2 Sphinx: 3.2.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 1.0.3 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.4 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.9.3 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.25.11 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.0 wheel-filename: 1.3.0 }}} " defect closed normal Volume Data fixed Tom Goddard all ChimeraX