Opened 6 years ago

Closed 6 years ago

#2558 closed defect (duplicate)

Wrong version of Clipper in ChimeraX 0.9

Reported by: peter.mace@… Owned by: Conrad Huang
Priority: normal Milestone:
Component: Tool Shed Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-06-06)
Description
New install of ChimeraX/iSolde on macbook pro with external GPU, error occurs when zooming in or out

Log:
UCSF ChimeraX version: 0.9 (2019-06-06)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 3wa9 format mmCIF fromDatabase pdb

3wa9 title:  
The nucleosome containing human H2A.Z.1 [more info...]  
  
Chain information for 3wa9 #1  
---  
Chain | Description  
A E | Histone H3.1  
B F | Histone H4  
C G | Histone H2A.Z  
D H | Histone H2B type 1-J  
I J | DNA (146-mer)  
  
  

> toolshed show ISOLDE

> set selectionWidth 4

3wa9 title:  
The nucleosome containing human H2A.Z.1 [more info...]  
  
Chain information for 3wa9  
---  
Chain | Description  
1.3/A 1.3/E | Histone H3.1  
1.3/B 1.3/F | Histone H4  
1.3/C 1.3/G | Histone H2A.Z  
1.3/D 1.3/H | Histone H2B type 1-J  
1.3/I 1.3/J | DNA (146-mer)  
  
Done loading forcefield  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/mousemodes.py", line 169, in zoom  
self.far_clip.plane_point = new_origin +
new_view_vec*(1+self.far_clip_multiplier)  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/mousemodes.py", line 113, in far_clip  
from chimerax.core.graphics.clipping import CameraClipPlane  
ModuleNotFoundError: No module named 'chimerax.core.graphics.clipping'  
  
ModuleNotFoundError: No module named 'chimerax.core.graphics.clipping'  
  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/mousemodes.py", line 113, in far_clip  
from chimerax.core.graphics.clipping import CameraClipPlane  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/mousemodes.py", line 169, in zoom  
self.far_clip.plane_point = new_origin +
new_view_vec*(1+self.far_clip_multiplier)  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/mousemodes.py", line 113, in far_clip  
from chimerax.core.graphics.clipping import CameraClipPlane  
ModuleNotFoundError: No module named 'chimerax.core.graphics.clipping'  
  
ModuleNotFoundError: No module named 'chimerax.core.graphics.clipping'  
  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/mousemodes.py", line 113, in far_clip  
from chimerax.core.graphics.clipping import CameraClipPlane  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/mousemodes.py", line 169, in zoom  
self.far_clip.plane_point = new_origin +
new_view_vec*(1+self.far_clip_multiplier)  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/mousemodes.py", line 113, in far_clip  
from chimerax.core.graphics.clipping import CameraClipPlane  
ModuleNotFoundError: No module named 'chimerax.core.graphics.clipping'  
  
ModuleNotFoundError: No module named 'chimerax.core.graphics.clipping'  
  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/mousemodes.py", line 113, in far_clip  
from chimerax.core.graphics.clipping import CameraClipPlane  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/mousemodes.py", line 169, in zoom  
self.far_clip.plane_point = new_origin +
new_view_vec*(1+self.far_clip_multiplier)  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/mousemodes.py", line 113, in far_clip  
from chimerax.core.graphics.clipping import CameraClipPlane  
ModuleNotFoundError: No module named 'chimerax.core.graphics.clipping'  
  
ModuleNotFoundError: No module named 'chimerax.core.graphics.clipping'  
  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/mousemodes.py", line 113, in far_clip  
from chimerax.core.graphics.clipping import CameraClipPlane  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/mousemodes.py", line 169, in zoom  
self.far_clip.plane_point = new_origin +
new_view_vec*(1+self.far_clip_multiplier)  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/mousemodes.py", line 113, in far_clip  
from chimerax.core.graphics.clipping import CameraClipPlane  
ModuleNotFoundError: No module named 'chimerax.core.graphics.clipping'  
  
ModuleNotFoundError: No module named 'chimerax.core.graphics.clipping'  
  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/mousemodes.py", line 113, in far_clip  
from chimerax.core.graphics.clipping import CameraClipPlane  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/mousemodes.py", line 169, in zoom  
self.far_clip.plane_point = new_origin +
new_view_vec*(1+self.far_clip_multiplier)  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/mousemodes.py", line 113, in far_clip  
from chimerax.core.graphics.clipping import CameraClipPlane  
ModuleNotFoundError: No module named 'chimerax.core.graphics.clipping'  
  
ModuleNotFoundError: No module named 'chimerax.core.graphics.clipping'  
  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/mousemodes.py", line 113, in far_clip  
from chimerax.core.graphics.clipping import CameraClipPlane  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/mousemodes.py", line 169, in zoom  
self.far_clip.plane_point = new_origin +
new_view_vec*(1+self.far_clip_multiplier)  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/mousemodes.py", line 113, in far_clip  
from chimerax.core.graphics.clipping import CameraClipPlane  
ModuleNotFoundError: No module named 'chimerax.core.graphics.clipping'  
  
ModuleNotFoundError: No module named 'chimerax.core.graphics.clipping'  
  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/mousemodes.py", line 113, in far_clip  
from chimerax.core.graphics.clipping import CameraClipPlane  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/mousemodes.py", line 169, in zoom  
self.far_clip.plane_point = new_origin +
new_view_vec*(1+self.far_clip_multiplier)  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/mousemodes.py", line 113, in far_clip  
from chimerax.core.graphics.clipping import CameraClipPlane  
ModuleNotFoundError: No module named 'chimerax.core.graphics.clipping'  
  
ModuleNotFoundError: No module named 'chimerax.core.graphics.clipping'  
  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/mousemodes.py", line 113, in far_clip  
from chimerax.core.graphics.clipping import CameraClipPlane  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/mousemodes.py", line 169, in zoom  
self.far_clip.plane_point = new_origin +
new_view_vec*(1+self.far_clip_multiplier)  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/mousemodes.py", line 113, in far_clip  
from chimerax.core.graphics.clipping import CameraClipPlane  
ModuleNotFoundError: No module named 'chimerax.core.graphics.clipping'  
  
ModuleNotFoundError: No module named 'chimerax.core.graphics.clipping'  
  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/mousemodes.py", line 113, in far_clip  
from chimerax.core.graphics.clipping import CameraClipPlane  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/mousemodes.py", line 169, in zoom  
self.far_clip.plane_point = new_origin +
new_view_vec*(1+self.far_clip_multiplier)  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/mousemodes.py", line 113, in far_clip  
from chimerax.core.graphics.clipping import CameraClipPlane  
ModuleNotFoundError: No module named 'chimerax.core.graphics.clipping'  
  
ModuleNotFoundError: No module named 'chimerax.core.graphics.clipping'  
  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/mousemodes.py", line 113, in far_clip  
from chimerax.core.graphics.clipping import CameraClipPlane  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/mousemodes.py", line 169, in zoom  
self.far_clip.plane_point = new_origin +
new_view_vec*(1+self.far_clip_multiplier)  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/mousemodes.py", line 113, in far_clip  
from chimerax.core.graphics.clipping import CameraClipPlane  
ModuleNotFoundError: No module named 'chimerax.core.graphics.clipping'  
  
ModuleNotFoundError: No module named 'chimerax.core.graphics.clipping'  
  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/mousemodes.py", line 113, in far_clip  
from chimerax.core.graphics.clipping import CameraClipPlane  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/mousemodes.py", line 169, in zoom  
self.far_clip.plane_point = new_origin +
new_view_vec*(1+self.far_clip_multiplier)  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/mousemodes.py", line 113, in far_clip  
from chimerax.core.graphics.clipping import CameraClipPlane  
ModuleNotFoundError: No module named 'chimerax.core.graphics.clipping'  
  
ModuleNotFoundError: No module named 'chimerax.core.graphics.clipping'  
  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/clipper/mousemodes.py", line 113, in far_clip  
from chimerax.core.graphics.clipping import CameraClipPlane  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.11.20
OpenGL renderer: AMD Radeon RX 570 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Change History (2)

comment:1 by Tristan Croll, 6 years ago

Component: Unassigned → Tool Shed
Owner: set to Conrad Huang
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Wrong version of Clipper in ChimeraX 0.9

This is due to a bug affecting installations in the ChimeraX 0.9 release, causing the wrong version of Clipper to be automatically installed on installing ISOLDE. I'd strongly recommend updating to the latest daily build of ChimeraX and reinstalling ISOLDE into that. This will give you the latest development version, with 4-5 months worth of bug fixes and enhancements to both ChimeraX and ISOLDE.

comment:2 by Tristan Croll, 6 years ago

Resolution: → duplicate
Status: assigned → closed
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