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Opened 6 years ago
Closed 6 years ago
#2181 closed defect (duplicate)
Choose box face: shapes not aligned
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Volume Data | Version: | 0.91 |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.17763
ChimeraX Version: 0.91 (2019-07-07)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 0.91 (2019-07-07)
© 2016-2019 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 6o85 format mmCIF fromDatabase pdb
6o85 title:
Electron cryo-microscopy of the eukaryotic translation initiation factor 2B
bound to eukaryotic translation initiation factor 2 from Homo sapiens [more
info...]
Chain information for 6o85 #1
---
Chain | Description
A B | Translation initiation factor eIF-2B subunit ε
C D | Translation initiation factor eIF-2B subunit β
E F | Translation initiation factor eIF-2B subunit δ
G H | Translation initiation factor eIF-2B subunit α
I J | Translation initiation factor eIF-2B subunit γ
L | Eukaryotic translation initiation factor 2 subunit 1
S | Eukaryotic translation initiation factor 2 subunit 3
d | Eukaryotic translation initiation factor 2 subunit β
Non-standard residues in 6o85 #1
---
C7B —
2-(4-chloranylphenoxy)-~{N}-[4-[2-(4-chloranylphenoxy)ethanoylamino]cyclohexyl]ethanamide
> open emdb:0651
Opened emd_0651.map, grid size 480,480,480, pixel 0.822, shown at level 0.174,
step 2, values float32
> style selAtoms stick
Changed 28546 atom styles
> volume transparency .70
> volume transparency .50
> volume transparency .60
> lighting full
> lighting soft
> lighting simple
> lighting full
> vr on
> lighting simple
started SteamVR rendering
> select clear
> vr oFF
> ui mousemode rightMode "contour level"
> volume #2 level 0.4812
> volume #2 level 0.3179
> ui mousemode rightMode "contour level"
> volume #2 level 0.4084
> volume #2 level -0.4612
> volume #2 level -0.5446
> volume #2 level -0.05125
> volume #2 level 0.2096
> volume #2 level 0.2274
> ui mousemode rightMode translate
> ui mousemode rightMode zoom
> ui mousemode rightMode tug
Missing atoms or parameterization needed by force field.
All heavy atoms and hydrogens with standard names are required.
Error with ignoreExternalBonds=False was
No template found for residue 1 (PRO). The set of atoms is similar to PRO, but
it is missing 7 hydrogen atoms.
Error with ignoreExternalBonds=True was
No template found for residue 1 (PRO). The set of atoms is similar to PRO, but
it is missing 7 hydrogen atoms.
> ui mousemode rightMode tug
Unknown command: addH
> addh
Summary of feedback from adding hydrogens to 6o85 #1
---
warnings | Not adding hydrogens to /A ARG 54 CZ because it is missing heavy-
atom bond partners
Not adding hydrogens to /A ARG 55 CZ because it is missing heavy-atom bond
partners
Not adding hydrogens to /A ARG 65 CZ because it is missing heavy-atom bond
partners
Not adding hydrogens to /A TYR 78 CZ because it is missing heavy-atom bond
partners
Not adding hydrogens to /A TRP 97 CZ2 because it is missing heavy-atom bond
partners
1355 messages similar to the above omitted
39 atoms were skipped as donors/acceptors due to missing heavy-atom bond
partners
notes | Termini for 6o85 (#1) chain A determined from SEQRES records
Termini for 6o85 (#1) chain B determined from SEQRES records
Termini for 6o85 (#1) chain C determined from SEQRES records
Termini for 6o85 (#1) chain D determined from SEQRES records
Termini for 6o85 (#1) chain E determined from SEQRES records
8 messages similar to the above omitted
Chain-initial residues that are actual N termini: /I MET 1, /J MET 1, /d UNK 3
Chain-initial residues that are not actual N termini: /A PRO 41, /B PRO 41, /B
ASP 549, /B ASP 692, /C GLY 8, /C TYR 126, /D GLY 8, /D HIS 125, /E GLN 166,
/F GLN 166, /G LYS 4, /G HIS 270, /H LYS 4, /H HIS 270, /I LEU 28, /I ARG 155,
/I LEU 258, /J LEU 28, /J ARG 155, /J LEU 258, /L LEU 3, /S LEU 20, /S ASN
123, /S HIS 184, /S LEU 228
Chain-final residues that are actual C termini: /C LEU 351, /D LEU 351, /G LEU
305, /H LEU 305, /d UNK 16
Chain-final residues that are not actual C termini: /A SER 466, /B SER 466, /B
ARG 688, /B GLU 715, /C GLY 98, /D GLY 98, /E ASP 522, /F ASP 522, /G TYR 252,
/H TYR 252, /I GLY 11, /I LYS 134, /I SER 238, /I ARG 295, /J GLY 11, /J LYS
134, /J SER 238, /J ARG 295, /L VAL 277, /S LEU 91, /S ILE 179, /S PRO 223, /S
THR 468
Missing OXT added to C-terminal residue /C LEU 351
Missing OXT added to C-terminal residue /D LEU 351
Missing OXT added to C-terminal residue /G LEU 305
Missing OXT added to C-terminal residue /H LEU 305
Missing OXT added to C-terminal residue /d UNK 16
2495 hydrogen bonds
Adding 'H' to /B ASP 549
Adding 'H' to /B ASP 692
Adding 'H' to /C GLY 8
Adding 'H' to /C TYR 126
Adding 'H' to /D GLY 8
18 messages similar to the above omitted
/A SER 466 is not terminus, removing H atom from 'C'
/B SER 466 is not terminus, removing H atom from 'C'
/B ARG 688 is not terminus, removing H atom from 'C'
/B GLU 715 is not terminus, removing H atom from 'C'
/C GLY 98 is not terminus, removing H atom from 'C'
18 messages similar to the above omitted
25468 hydrogens added
> ui mousemode rightMode tug
Missing atoms or parameterization needed by force field.
All heavy atoms and hydrogens with standard names are required.
Error with ignoreExternalBonds=False was
No template found for residue 1 (PRO). The set of atoms matches PRO, but the
bonds are different. Perhaps the chain is missing a terminal group?
Error with ignoreExternalBonds=True was
No template found for residue 14 (ARG). The set of atoms is similar to LYN,
but it is missing 3 hydrogen atoms.
> ui mousemode rightMode "clip rotate"
> ui mousemode rightMode "move planes"
> volume #2 region 242,0,0,242,479,479
> ui mousemode rightMode "crop volume"
> ui mousemode rightMode "contour level"
> volume #2 level 0.5899
> ui mousemode rightMode zoom
> ui mousemode rightMode "crop volume"
Traceback (most recent call last):
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 452, in <lambda>
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 381, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 34, in mouse_down
self._choose_box_face(line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 40, in _choose_box_face
v, self.axis, self.side, self.ijk = nearest_volume_face(line, maps)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 174, in nearest_volume_face
ijk, axis, side = face_intercept(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 198, in face_intercept
ijk_in, ijk_out = volume_index_segment(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 288, in volume_index_segment
volume.ijk_bounds(), clipping_model)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 24, in box_intercepts
bline = line_to_box_transform * line
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\place.py", line 120, in __mul__
return m34.apply_matrix(self._matrix, p)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 453, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 381, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 60, in mouse_drag
self.mouse_down(event)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 34, in mouse_down
self._choose_box_face(line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 40, in _choose_box_face
v, self.axis, self.side, self.ijk = nearest_volume_face(line, maps)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 174, in nearest_volume_face
ijk, axis, side = face_intercept(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 198, in face_intercept
ijk_in, ijk_out = volume_index_segment(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 288, in volume_index_segment
volume.ijk_bounds(), clipping_model)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 24, in box_intercepts
bline = line_to_box_transform * line
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\place.py", line 120, in __mul__
return m34.apply_matrix(self._matrix, p)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 453, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 381, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 60, in mouse_drag
self.mouse_down(event)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 34, in mouse_down
self._choose_box_face(line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 40, in _choose_box_face
v, self.axis, self.side, self.ijk = nearest_volume_face(line, maps)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 174, in nearest_volume_face
ijk, axis, side = face_intercept(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 198, in face_intercept
ijk_in, ijk_out = volume_index_segment(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 288, in volume_index_segment
volume.ijk_bounds(), clipping_model)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 24, in box_intercepts
bline = line_to_box_transform * line
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\place.py", line 120, in __mul__
return m34.apply_matrix(self._matrix, p)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 453, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 381, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 60, in mouse_drag
self.mouse_down(event)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 34, in mouse_down
self._choose_box_face(line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 40, in _choose_box_face
v, self.axis, self.side, self.ijk = nearest_volume_face(line, maps)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 174, in nearest_volume_face
ijk, axis, side = face_intercept(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 198, in face_intercept
ijk_in, ijk_out = volume_index_segment(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 288, in volume_index_segment
volume.ijk_bounds(), clipping_model)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 24, in box_intercepts
bline = line_to_box_transform * line
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\place.py", line 120, in __mul__
return m34.apply_matrix(self._matrix, p)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 453, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 381, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 60, in mouse_drag
self.mouse_down(event)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 34, in mouse_down
self._choose_box_face(line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 40, in _choose_box_face
v, self.axis, self.side, self.ijk = nearest_volume_face(line, maps)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 174, in nearest_volume_face
ijk, axis, side = face_intercept(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 198, in face_intercept
ijk_in, ijk_out = volume_index_segment(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 288, in volume_index_segment
volume.ijk_bounds(), clipping_model)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 24, in box_intercepts
bline = line_to_box_transform * line
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\place.py", line 120, in __mul__
return m34.apply_matrix(self._matrix, p)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 453, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 381, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 60, in mouse_drag
self.mouse_down(event)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 34, in mouse_down
self._choose_box_face(line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 40, in _choose_box_face
v, self.axis, self.side, self.ijk = nearest_volume_face(line, maps)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 174, in nearest_volume_face
ijk, axis, side = face_intercept(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 198, in face_intercept
ijk_in, ijk_out = volume_index_segment(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 288, in volume_index_segment
volume.ijk_bounds(), clipping_model)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 24, in box_intercepts
bline = line_to_box_transform * line
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\place.py", line 120, in __mul__
return m34.apply_matrix(self._matrix, p)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 453, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 381, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 60, in mouse_drag
self.mouse_down(event)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 34, in mouse_down
self._choose_box_face(line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 40, in _choose_box_face
v, self.axis, self.side, self.ijk = nearest_volume_face(line, maps)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 174, in nearest_volume_face
ijk, axis, side = face_intercept(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 198, in face_intercept
ijk_in, ijk_out = volume_index_segment(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 288, in volume_index_segment
volume.ijk_bounds(), clipping_model)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 24, in box_intercepts
bline = line_to_box_transform * line
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\place.py", line 120, in __mul__
return m34.apply_matrix(self._matrix, p)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 453, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 381, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 60, in mouse_drag
self.mouse_down(event)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 34, in mouse_down
self._choose_box_face(line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 40, in _choose_box_face
v, self.axis, self.side, self.ijk = nearest_volume_face(line, maps)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 174, in nearest_volume_face
ijk, axis, side = face_intercept(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 198, in face_intercept
ijk_in, ijk_out = volume_index_segment(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 288, in volume_index_segment
volume.ijk_bounds(), clipping_model)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 24, in box_intercepts
bline = line_to_box_transform * line
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\place.py", line 120, in __mul__
return m34.apply_matrix(self._matrix, p)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 453, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 381, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 60, in mouse_drag
self.mouse_down(event)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 34, in mouse_down
self._choose_box_face(line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 40, in _choose_box_face
v, self.axis, self.side, self.ijk = nearest_volume_face(line, maps)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 174, in nearest_volume_face
ijk, axis, side = face_intercept(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 198, in face_intercept
ijk_in, ijk_out = volume_index_segment(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 288, in volume_index_segment
volume.ijk_bounds(), clipping_model)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 24, in box_intercepts
bline = line_to_box_transform * line
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\place.py", line 120, in __mul__
return m34.apply_matrix(self._matrix, p)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 453, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 381, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 60, in mouse_drag
self.mouse_down(event)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 34, in mouse_down
self._choose_box_face(line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 40, in _choose_box_face
v, self.axis, self.side, self.ijk = nearest_volume_face(line, maps)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 174, in nearest_volume_face
ijk, axis, side = face_intercept(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 198, in face_intercept
ijk_in, ijk_out = volume_index_segment(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 288, in volume_index_segment
volume.ijk_bounds(), clipping_model)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 24, in box_intercepts
bline = line_to_box_transform * line
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\place.py", line 120, in __mul__
return m34.apply_matrix(self._matrix, p)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 453, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 381, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 60, in mouse_drag
self.mouse_down(event)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 34, in mouse_down
self._choose_box_face(line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 40, in _choose_box_face
v, self.axis, self.side, self.ijk = nearest_volume_face(line, maps)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 174, in nearest_volume_face
ijk, axis, side = face_intercept(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 198, in face_intercept
ijk_in, ijk_out = volume_index_segment(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 288, in volume_index_segment
volume.ijk_bounds(), clipping_model)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 24, in box_intercepts
bline = line_to_box_transform * line
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\place.py", line 120, in __mul__
return m34.apply_matrix(self._matrix, p)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 453, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 381, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 60, in mouse_drag
self.mouse_down(event)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 34, in mouse_down
self._choose_box_face(line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 40, in _choose_box_face
v, self.axis, self.side, self.ijk = nearest_volume_face(line, maps)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 174, in nearest_volume_face
ijk, axis, side = face_intercept(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 198, in face_intercept
ijk_in, ijk_out = volume_index_segment(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 288, in volume_index_segment
volume.ijk_bounds(), clipping_model)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 24, in box_intercepts
bline = line_to_box_transform * line
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\place.py", line 120, in __mul__
return m34.apply_matrix(self._matrix, p)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 453, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 381, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 60, in mouse_drag
self.mouse_down(event)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 34, in mouse_down
self._choose_box_face(line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 40, in _choose_box_face
v, self.axis, self.side, self.ijk = nearest_volume_face(line, maps)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 174, in nearest_volume_face
ijk, axis, side = face_intercept(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 198, in face_intercept
ijk_in, ijk_out = volume_index_segment(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 288, in volume_index_segment
volume.ijk_bounds(), clipping_model)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 24, in box_intercepts
bline = line_to_box_transform * line
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\place.py", line 120, in __mul__
return m34.apply_matrix(self._matrix, p)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 453, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 381, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 60, in mouse_drag
self.mouse_down(event)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 34, in mouse_down
self._choose_box_face(line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 40, in _choose_box_face
v, self.axis, self.side, self.ijk = nearest_volume_face(line, maps)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 174, in nearest_volume_face
ijk, axis, side = face_intercept(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 198, in face_intercept
ijk_in, ijk_out = volume_index_segment(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 288, in volume_index_segment
volume.ijk_bounds(), clipping_model)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 24, in box_intercepts
bline = line_to_box_transform * line
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\place.py", line 120, in __mul__
return m34.apply_matrix(self._matrix, p)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 453, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 381, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 60, in mouse_drag
self.mouse_down(event)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 34, in mouse_down
self._choose_box_face(line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 40, in _choose_box_face
v, self.axis, self.side, self.ijk = nearest_volume_face(line, maps)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 174, in nearest_volume_face
ijk, axis, side = face_intercept(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 198, in face_intercept
ijk_in, ijk_out = volume_index_segment(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 288, in volume_index_segment
volume.ijk_bounds(), clipping_model)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 24, in box_intercepts
bline = line_to_box_transform * line
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\place.py", line 120, in __mul__
return m34.apply_matrix(self._matrix, p)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 453, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 381, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 60, in mouse_drag
self.mouse_down(event)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 34, in mouse_down
self._choose_box_face(line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 40, in _choose_box_face
v, self.axis, self.side, self.ijk = nearest_volume_face(line, maps)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 174, in nearest_volume_face
ijk, axis, side = face_intercept(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 198, in face_intercept
ijk_in, ijk_out = volume_index_segment(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 288, in volume_index_segment
volume.ijk_bounds(), clipping_model)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 24, in box_intercepts
bline = line_to_box_transform * line
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\place.py", line 120, in __mul__
return m34.apply_matrix(self._matrix, p)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 453, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 381, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 60, in mouse_drag
self.mouse_down(event)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 34, in mouse_down
self._choose_box_face(line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 40, in _choose_box_face
v, self.axis, self.side, self.ijk = nearest_volume_face(line, maps)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 174, in nearest_volume_face
ijk, axis, side = face_intercept(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 198, in face_intercept
ijk_in, ijk_out = volume_index_segment(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 288, in volume_index_segment
volume.ijk_bounds(), clipping_model)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 24, in box_intercepts
bline = line_to_box_transform * line
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\place.py", line 120, in __mul__
return m34.apply_matrix(self._matrix, p)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 453, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 381, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 60, in mouse_drag
self.mouse_down(event)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 34, in mouse_down
self._choose_box_face(line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 40, in _choose_box_face
v, self.axis, self.side, self.ijk = nearest_volume_face(line, maps)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 174, in nearest_volume_face
ijk, axis, side = face_intercept(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 198, in face_intercept
ijk_in, ijk_out = volume_index_segment(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 288, in volume_index_segment
volume.ijk_bounds(), clipping_model)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 24, in box_intercepts
bline = line_to_box_transform * line
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\place.py", line 120, in __mul__
return m34.apply_matrix(self._matrix, p)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 453, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 381, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 60, in mouse_drag
self.mouse_down(event)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 34, in mouse_down
self._choose_box_face(line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 40, in _choose_box_face
v, self.axis, self.side, self.ijk = nearest_volume_face(line, maps)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 174, in nearest_volume_face
ijk, axis, side = face_intercept(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 198, in face_intercept
ijk_in, ijk_out = volume_index_segment(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 288, in volume_index_segment
volume.ijk_bounds(), clipping_model)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 24, in box_intercepts
bline = line_to_box_transform * line
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\place.py", line 120, in __mul__
return m34.apply_matrix(self._matrix, p)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 453, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 381, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 60, in mouse_drag
self.mouse_down(event)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 34, in mouse_down
self._choose_box_face(line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 40, in _choose_box_face
v, self.axis, self.side, self.ijk = nearest_volume_face(line, maps)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 174, in nearest_volume_face
ijk, axis, side = face_intercept(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 198, in face_intercept
ijk_in, ijk_out = volume_index_segment(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 288, in volume_index_segment
volume.ijk_bounds(), clipping_model)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 24, in box_intercepts
bline = line_to_box_transform * line
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\place.py", line 120, in __mul__
return m34.apply_matrix(self._matrix, p)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 453, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 381, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 60, in mouse_drag
self.mouse_down(event)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 34, in mouse_down
self._choose_box_face(line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 40, in _choose_box_face
v, self.axis, self.side, self.ijk = nearest_volume_face(line, maps)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 174, in nearest_volume_face
ijk, axis, side = face_intercept(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 198, in face_intercept
ijk_in, ijk_out = volume_index_segment(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 288, in volume_index_segment
volume.ijk_bounds(), clipping_model)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 24, in box_intercepts
bline = line_to_box_transform * line
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\place.py", line 120, in __mul__
return m34.apply_matrix(self._matrix, p)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 453, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 381, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 60, in mouse_drag
self.mouse_down(event)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 34, in mouse_down
self._choose_box_face(line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 40, in _choose_box_face
v, self.axis, self.side, self.ijk = nearest_volume_face(line, maps)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 174, in nearest_volume_face
ijk, axis, side = face_intercept(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 198, in face_intercept
ijk_in, ijk_out = volume_index_segment(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 288, in volume_index_segment
volume.ijk_bounds(), clipping_model)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 24, in box_intercepts
bline = line_to_box_transform * line
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\place.py", line 120, in __mul__
return m34.apply_matrix(self._matrix, p)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 453, in <lambda>
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 381, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 60, in mouse_drag
self.mouse_down(event)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 34, in mouse_down
self._choose_box_face(line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\moveplanes.py", line 40, in _choose_box_face
v, self.axis, self.side, self.ijk = nearest_volume_face(line, maps)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 174, in nearest_volume_face
ijk, axis, side = face_intercept(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 198, in face_intercept
ijk_in, ijk_out = volume_index_segment(v, line)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 288, in volume_index_segment
volume.ijk_bounds(), clipping_model)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\map\slice.py", line 24, in box_intercepts
bline = line_to_box_transform * line
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\place.py", line 120, in __mul__
return m34.apply_matrix(self._matrix, p)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
ValueError: shapes (2,) and (3,3) not aligned: 2 (dim 0) != 3 (dim 0)
File "C:\Program Files\ChimeraXdaily\bin\lib\site-
packages\chimerax\core\geometry\matrix.py", line 22, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 399.24
OpenGL renderer: GeForce GTX 980 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Change History (2)
comment:1 by , 6 years ago
| Component: | Unassigned → Volume Data |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Choose box face: shapes not aligned |
| Version: | → 0.91 |
comment:2 by , 6 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Duplicate of #2163. Reported by Adam Frost.