Opened 7 years ago

Closed 7 years ago

#1712 closed defect (can't reproduce)

Image save: Require contiguous 3x4 array

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Graphics Version: 0.8
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-18.2.0-x86_64-i386-64bit
ChimeraX Version: 0.8 (2018-10-11)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.8 (2018-10-11)  
How to cite UCSF ChimeraX  

open p97_p47-1s3s.pdb

p97_p47-1s3s.pdb title:  
Crystal structure of aaa atpase P97/VCP ND1 In complex with P47 C
[more info...]  
  
Chain information for p97_p47-1s3s.pdb #1  
---  
Chain | Description  
A B C D E F | transitional endoplasmic reticulum atpase (ter atpase) (15S
Mg(2+)- atpase P97 subunit) (valosin containing protein) (VCP) [contains:
valosin]  
G H I | P47 protein  
  

hide selAtoms ↵

show selAtoms ribbons

select /H

761 atoms, 764 bonds, 1 pseudobond, 1 model selected  

hide selAtoms ribbons ↵

select /I

156 atoms, 154 bonds, 1 pseudobond, 1 model selected  

hide selAtoms ribbons ↵

select /G

827 atoms, 833 bonds selected  

select /A-E

17150 atoms, 17381 bonds selected  

color /A-E grey

select /F:1-180

1290 atoms, 1310 bonds selected  

color /F:1-190 light green

color /F:191-400 peachpuff

color show

Illegal color name: ""  

color show 223,105,165

Illegal color name: "223,105,165"  

color /G #df69a5

lighting soft

lighting flat

set silhouettes false

set silhouettes true

save /Users/Po-Lin/Desktop/image1.png supersample 3

turn x 90

turn x 90

turn x 90

turn x 90

turn z -60

save /Users/Po-Lin/Desktop/image1.png supersample 3

turn x -90

turn y 60

turn y -120

save /Users/Po-Lin/Desktop/image1.png supersample 3

show selAtoms surfaces

transparency s 50

Missing or invalid "percent" argument: Expected a number  

hide #!1.2 models ↵

show #!1.2 models

transparency #1.2-1.3 50

transparency #1.2 50

transparency #1.3 50

color #1.2 light green target s

transparency #1.2 50

transparency #1.2 60

transparency #1.2 70

color #1.3 #df69a5 target s

transparency #1.3 70

show selAtoms

transparency #1.3 70

transparency #1.3 70 target s

style selAtoms stick

Changed 790 atom styles  

color selAtoms byhetero

color selAtoms bychain

color #1.2 light green target a byelement

Expected a keyword  

color #1.2 byelement target a

color #1.2 byelement target a

hide surfaces ↵

color selAtoms byhetero

select /F:1-190

1367 atoms, 1389 bonds selected  

color /F:1-190

color /F:1-190 light green

color /F:1-190 byelement target a

color /G byelement target a

color /G #df69a5

color /G #df69a5 target a

color /G byelement target a

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

save session /Users/Po-
Lin/Dropbox/Projects/p97/p47_coord/p47_p97_interaction_1s3s.cxs

Session file format is not finalized, and thus might not be restorable in
other versions of ChimeraX.  

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

hide selAtoms ↵

movie record

turn y 2 180

wait 180

movie encode /Users/Po-Lin/Desktop/movie1.mp4

An error occurred during encoding. See Reply Log for details.  
  
Error during MPEG encoding:  
\-----------------------------  
Exit value: -1  
Error message:  
Could not find ffmpeg executable at ffmpeg  
\-----------------------------  
  

could not retrieve bundle list from toolshed  

rock y 10

Unknown command: rock y 10  

save session /Users/Po-
Lin/Dropbox/Projects/p97/p47_coord/p47_p97_interaction_1s3s.cxs

Session file format is not finalized, and thus might not be restorable in
other versions of ChimeraX.  

hide /A-E ↵

select /A-E

17150 atoms, 17381 bonds selected  

hide selAtoms ribbons ↵

select /F:191-

Expected an objects specifier or a keyword  

select /F:191-400

1629 atoms, 1654 bonds selected  

hide selAtoms ribbons ↵

select /F:191-600

2065 atoms, 2095 bonds selected  

hide selAtoms ribbons ↵

lighting full

An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.  
  
Traceback (most recent call last):  
File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/updateloop.py", line 72, in draw_new_frame  
view.draw(check_for_changes = False)  
File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/graphics/view.py", line 157, in draw  
self._draw_scene(camera, drawings)  
File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/graphics/view.py", line 186, in _draw_scene  
shadow, multishadow = self._compute_shadowmaps(opaque_drawings +
transparent_drawings, camera)  
File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/graphics/view.py", line 511, in _compute_shadowmaps  
shadow_enabled = r.shadow.use_shadow_map(camera, drawings,
self._shadow_bounds)  
File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/graphics/opengl.py", line 1166, in use_shadow_map  
center, radius, sdrawings = shadow_bounds(drawings)  
File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/graphics/view.py", line 522, in _shadow_bounds  
b = bounds.union_bounds(d.bounds() for d in sdrawings)  
File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/geometry/bounds.py", line 90, in union_bounds  
for b in blist:  
File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/graphics/view.py", line 522, in <genexpr>  
b = bounds.union_bounds(d.bounds() for d in sdrawings)  
File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 867, in bounds  
spos = self.get_scene_positions(displayed_only=True)  
File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 445, in get_scene_positions  
p = d.get_positions(displayed_only) * p  
File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/geometry/place.py", line 541, in __mul__  
pp.append(p*p2)  
File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/geometry/place.py", line 95, in __mul__  
return Place(_geometry.multiply_matrices_f64(self.matrix, p.matrix))  
TypeError: Require contiguous 3x4 array  
  

save session /Users/Po-
Lin/Dropbox/Projects/p97/p47_coord/p47_p97_interaction_1s3s-focus.cxs

Session file format is not finalized, and thus might not be restorable in
other versions of ChimeraX.  

Traceback (most recent call last):  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/ui/gui.py", line 782, in <lambda>  
    save_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_save_cb(sess))  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/ui/gui.py", line 557, in file_save_cb  
    self.save_dialog.display(self, session)  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/ui/save_dialog.py", line 141, in display  
    fmt.save(session, filename)  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/ui/save_dialog.py", line 40, in save  
    return self._save(session, filename)  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/ui/save_dialog.py", line 93, in _session_save  
    run(session, "save session %s" % quote_if_necessary(filename))  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/commands/run.py", line 31, in run  
    results = command.run(text, log=log)  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2562, in run  
    result = ci.function(session, **kw_args)  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/session.py", line 913, in save_session  
    save(session, filename, **kw)  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/commands/save.py", line 61, in save  
    fmt.export(session, filename, fmt.nicknames[0], **kw)  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/io.py", line 198, in export  
    result = self.export_func(session, path, **kw)  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/session.py", line 740, in save  
    image = session.main_view.image(width, height)  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/graphics/view.py", line 393, in image  
    self.draw(c, drawings, swap_buffers = False)  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/graphics/view.py", line 157, in draw  
    self._draw_scene(camera, drawings)  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/graphics/view.py", line 186, in _draw_scene  
    shadow, multishadow = self._compute_shadowmaps(opaque_drawings +
transparent_drawings, camera)  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/graphics/view.py", line 511, in _compute_shadowmaps  
    shadow_enabled = r.shadow.use_shadow_map(camera, drawings,
self._shadow_bounds)  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/graphics/opengl.py", line 1166, in use_shadow_map  
    center, radius, sdrawings = shadow_bounds(drawings)  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/graphics/view.py", line 522, in _shadow_bounds  
    b = bounds.union_bounds(d.bounds() for d in sdrawings)  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/geometry/bounds.py", line 90, in union_bounds  
    for b in blist:  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/graphics/view.py", line 522, in <genexpr>  
    b = bounds.union_bounds(d.bounds() for d in sdrawings)  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 867, in bounds  
    spos = self.get_scene_positions(displayed_only=True)  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 445, in get_scene_positions  
    p = d.get_positions(displayed_only) * p  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/geometry/place.py", line 541, in __mul__  
    pp.append(p*p2)  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/geometry/place.py", line 95, in __mul__  
    return Place(_geometry.multiply_matrices_f64(self.matrix, p.matrix))  
TypeError: Require contiguous 3x4 array  
  
TypeError: Require contiguous 3x4 array  
  
File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/geometry/place.py", line 95, in __mul__  
return Place(_geometry.multiply_matrices_f64(self.matrix, p.matrix))  
  
See log for complete Python traceback.  
  

save /Users/Po-Lin/Desktop/image1.png supersample 3

Traceback (most recent call last):  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/shortcuts/tool.py", line 50, in button_press_cb  
    ks.run_shortcut(keys)  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/shortcuts/shortcuts.py", line 375, in run_shortcut  
    sc.run(self.session, status = self._enabled)  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/shortcuts/shortcuts.py", line 294, in run  
    f(s)  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/shortcuts/shortcuts.py", line 1015, in save_image  
    run(session, cmd)  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/commands/run.py", line 31, in run  
    results = command.run(text, log=log)  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2562, in run  
    result = ci.function(session, **kw_args)  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/commands/save.py", line 61, in save  
    fmt.export(session, filename, fmt.nicknames[0], **kw)  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/io.py", line 198, in export  
    result = self.export_func(session, path, **kw)  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/image.py", line 149, in save_image  
    transparent_background=transparent_background)  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/graphics/view.py", line 404, in image  
    self.draw(c, drawings, swap_buffers = False)  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/graphics/view.py", line 157, in draw  
    self._draw_scene(camera, drawings)  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/graphics/view.py", line 186, in _draw_scene  
    shadow, multishadow = self._compute_shadowmaps(opaque_drawings +
transparent_drawings, camera)  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/graphics/view.py", line 511, in _compute_shadowmaps  
    shadow_enabled = r.shadow.use_shadow_map(camera, drawings,
self._shadow_bounds)  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/graphics/opengl.py", line 1166, in use_shadow_map  
    center, radius, sdrawings = shadow_bounds(drawings)  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/graphics/view.py", line 522, in _shadow_bounds  
    b = bounds.union_bounds(d.bounds() for d in sdrawings)  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/geometry/bounds.py", line 90, in union_bounds  
    for b in blist:  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/graphics/view.py", line 522, in <genexpr>  
    b = bounds.union_bounds(d.bounds() for d in sdrawings)  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 867, in bounds  
    spos = self.get_scene_positions(displayed_only=True)  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 445, in get_scene_positions  
    p = d.get_positions(displayed_only) * p  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/geometry/place.py", line 541, in __mul__  
    pp.append(p*p2)  
  File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/geometry/place.py", line 95, in __mul__  
    return Place(_geometry.multiply_matrices_f64(self.matrix, p.matrix))  
TypeError: Require contiguous 3x4 array  
  
TypeError: Require contiguous 3x4 array  
  
File "/Applications/ChimeraX.app/Contents/lib/python3.6/site-
packages/chimerax/core/geometry/place.py", line 95, in __mul__  
return Place(_geometry.multiply_matrices_f64(self.matrix, p.matrix))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.4.10
OpenGL renderer: AMD Radeon R9 M390 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Change History (2)

comment:1 by Eric Pettersen, 7 years ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Image save: Require contiguous 3x4 array
Version: → 0.8

comment:2 by Tom Goddard, 7 years ago

Resolution: → can't reproduce
Status: assigned → closed

Bug in 0.8. Does not appear possible to have non-contiguous matrix in Place in current code.

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