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Opened 4 years ago
Closed 3 years ago
#4721 closed defect (fixed)
tilted slab: 'numpy.ndarray' object is not callable
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Volume Data | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x7ff75bf3a220> ->
<chimerax.surface.dust.Redust object at 0x7ff75f1c6fd0> ->
<chimerax.clipper.maps.map_handler_base.FastVolumeSurface object at
0x7ff75e84af70> 'surface' -> <chimerax.clipper.maps.xmapset.XmapHandler_Static
object at 0x7ff75dfda220> '(STATIC) (Fourier-map-coefficients)
2FOFCWT_no_fill, PH2FOFCWT_no_fill' ->
<chimerax.clipper.clipper_python.data32.HKL_data_F_phi_float object at
0x7ff75dfbb770>". Session might not restore properly.
Unable to save '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x7ff75bf3a220> ->
<chimerax.surface.dust.Redust object at 0x7ff74fea1d90> ->
<chimerax.clipper.maps.map_handler_base.FastVolumeSurface object at
0x7ff75e84aa30> 'surface' -> <chimerax.clipper.maps.xmapset.XmapHandler_Static
object at 0x7ff75df9a910> '(STATIC) (Model-structure-factors-(bulk-solvent-
and-all-scales-included)) F-model, PHIF-model' ->
<chimerax.clipper.clipper_python.data32.HKL_data_F_phi_float object at
0x7ff75d1178b0>". Session might not restore properly.
Unable to save '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x7ff75bf3a220> ->
<chimerax.surface.dust.Redust object at 0x7ff75f1c6f10> ->
<chimerax.clipper.maps.map_handler_base.FastVolumeSurface object at
0x7ff75e859070> 'surface' -> <chimerax.clipper.maps.xmapset.XmapHandler_Static
object at 0x7ff75dfda430> '(STATIC) (Fourier-map-coefficients) FOFCWT,
PHFOFCWT' -> <chimerax.clipper.clipper_python.data32.HKL_data_F_phi_float
object at 0x7ff75dfbb830>". Session might not restore properly.
Unable to save '_surface_updaters' ->
<chimerax.surface.updaters.SurfaceUpdaters object at 0x7ff75bf3a220> ->
<chimerax.surface.dust.Redust object at 0x7ff74fea1f10> ->
<chimerax.clipper.maps.map_handler_base.FastVolumeSurface object at
0x7ff75e8595e0> 'surface' -> <chimerax.clipper.maps.xmapset.XmapHandler_Static
object at 0x7ff75e84a1f0> '(STATIC) (Fourier-map-coefficients) 2FOFCWT,
PH2FOFCWT' -> <chimerax.clipper.clipper_python.data32.HKL_data_F_phi_float
object at 0x7ff75cdf1a70>". 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 <lambda>
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 <lambda>
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 <lambda>
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 <lambda>
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 <lambda>
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 <lambda>
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 <lambda>
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 <lambda>
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 <lambda>
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 <lambda>
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 <lambda>
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 <lambda>
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 <lambda>
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 <lambda>
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 <lambda>
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 <lambda>
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 <lambda>
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 <lambda>
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 <lambda>
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 <lambda>
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 <lambda>
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 <lambda>
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 <lambda>
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 <lambda>
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 <lambda>
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 <lambda>
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 <lambda>
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 <lambda>
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
Change History (5)
comment:1 by , 4 years ago
| Component: | Unassigned → Volume Data |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → tilted slab: 'numpy.ndarray' object is not callable |
comment:2 by , 4 years ago
| Cc: | added |
|---|---|
| Owner: | changed from to |
comment:3 by , 4 years ago
Made MapHandlerBase.center a method rather than property. I think I still need the override, though: since a crystallographic map is effectively infinite, the only really sensible definition for "center" is "the center of the part that's shown right now". Then, to maintain consistency, I think non-crystallographic maps should behave the same way. Open to suggestions, of course. With the change, the "tilted slab" mode does work mostly correctly (with the exception that in Spotlight mode, it doesn't move when the spotlight center is moved normal to the slab). This isn't something I ever really envisaged being used with Clipper, though.
There are a few other issues for me to handle in this bug report:
- the user is using "vop gaussian" on a crystallographic map. That generally won't work so well, since the command will only see the portion of the map that's currently displayed. Sharpening/smoothing of these maps should really happen via the Clipper engine to make sure it's always using the full dataset. All the pieces are actually there to provide a user-adjustable "smoothness" level for a given crystal map... will just take some coding to make it available. Would be good (and quite popular, I think) to have a similar dynamic sharpening/smoothing functionality for cryo-EM maps (i.e. where the original data is kept undisturbed, but what is shown is the data convolved with the appropriate Gaussian).
- "Static" crystallographic maps (generated from precalculated amplitudes and phases) are failing to save in sessions. Will look into why that is, and fix.
comment:4 by , 4 years ago
Sounds reasonable that your subclass of Volume to handle extending an X-ray unit cell map to infinity needs to define center() to something and probably center of currently displayed region is best. It looks to me that the Volume code does define center() as the center of the displayed region unless you provide the "subregion" argument. I wouldn't worry too much about the behavior of tilted slab combined with spotlight as long as it doesn't throw errors.
For the dynamic map smoothing I am not a fan of building rendering of a smoothed version into the unsmoothed map. This adds too much complexity. The widely used ChimeraX paradigm is that smoothing will create a new map (the "smoothed map") and that smoothed map can be recomputed dynamically as the user adjusts a B-factor.
For session saving -- yeah, that is a small disaster if session saving fails. Our session saving is very brittle -- worse than in Chimera. Let me know if you have ideas to make it more robust.
comment:5 by , 3 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Closing this, since the headline errors are fixed. I'd still like to add dynamic sharpening/smoothing to Clipper's crystallographic maps, but that can wait until a later date.
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This error using the tilted slab mouse mode is caused by a problem in the Clipper module used by ISOLDE. It defines class MapHandlerBase(Volume): with a "center" property that overrides the Volume center() method. The rotated slab code is trying to call the center method, but instead gets a numpy array causing the error. The MapHandlerBase should not override the Volume center method.