Opened 6 years ago

Closed 6 years ago

Last modified 6 years ago

#2347 closed defect (duplicate)

Wrong version of Clipper installed

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

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.17134
ChimeraX Version: 0.9 (2019-06-06)
Description
using mouse scroll wheel
(Describe the actions that caused this problem to occur here)

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  
Downloading bundle ChimeraX_ISOLDE-1.0b3-cp37-cp37m-win_amd64.whl  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing
c:\users\joel\downloads\chimerax_isolde-1.0b3-cp37-cp37m-win_amd64.whl  
Collecting ChimeraX-Clipper>=0.9.4 (from ChimeraX-ISOLDE==1.0b3)  
Downloading
https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxclipper/releases/0.9.7/ChimeraX_Clipper-0.9.7-cp37-cp37m-win_amd64.whl
(22.0MB)  
Requirement already satisfied, skipping upgrade: ChimeraX-Core==0.9 in
c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.0b3)
(0.9)  
Requirement already satisfied, skipping upgrade: ChimeraX-Atomic>=0.7 in
c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.0b3)
(1.0)  
Installing collected packages: ChimeraX-Clipper, ChimeraX-ISOLDE  
chimerax-clipper 0.9.7 has requirement ChimeraX-Core==0.91, but you'll have
chimerax-core 0.9 which is incompatible.  
Could not install packages due to an EnvironmentError: [WinError 5] Access is
denied: 'C:\\\Program Files\\\ChimeraX\\\bin\\\Lib\\\site-
packages\\\chimerax\\\clipper'  
Consider using the `--user` option or check the permissions.  
  
You are using pip version 19.0.3, however version 19.2.2 is available.  
You should consider upgrading via the 'python -m pip install --upgrade pip'
command.  
  
Downloading bundle ChimeraX_ISOLDE-1.0b3-cp37-cp37m-win_amd64.whl  
Successfully installed ChimeraX-Clipper-0.9.7 ChimeraX-ISOLDE-1.0b3  
Installed ChimeraX-Clipper (0.9.7)  
Installed ChimeraX-ISOLDE (1.0b3)  

> help help:quickstart

> toolshed show ISOLDE

> set selectionWidth 4

Done loading forcefield  

> open C:/Users/joel/Desktop/temp/cluster1_1.pdb

Summary of feedback from opening C:/Users/joel/Desktop/temp/cluster1_1.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK FILENAME="complex_4w.pdb0"  
  
Ignored bad PDB record found on line 2  
REMARK ===============================================================  
  
Ignored bad PDB record found on line 3  
REMARK HADDOCK run for complex  
  
Ignored bad PDB record found on line 4  
REMARK initial structure: complex_4.pdb  
  
Ignored bad PDB record found on line 5  
REMARK ===============================================================  
  
33 messages similar to the above omitted  
  
Chain information for cluster1_1.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  
Chain information for cluster1_1.pdb  
---  
Chain | Description  
1.3/A | No description available  
1.3/B | No description available  
1.3/C | No description available  
1.3/D | No description available  
1.3/E | No description available  
1.3/F | No description available  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\clipper\mousemodes.py", line 168, in zoom  
self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier)  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\clipper\mousemodes.py", line 168, in zoom  
self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier)  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\clipper\mousemodes.py", line 168, in zoom  
self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier)  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\clipper\mousemodes.py", line 168, in zoom  
self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier)  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\clipper\mousemodes.py", line 168, in zoom  
self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier)  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\clipper\mousemodes.py", line 168, in zoom  
self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier)  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\clipper\mousemodes.py", line 168, in zoom  
self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier)  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\clipper\mousemodes.py", line 168, in zoom  
self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier)  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\clipper\mousemodes.py", line 168, in zoom  
self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier)  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\clipper\mousemodes.py", line 168, in zoom  
self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier)  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\clipper\mousemodes.py", line 168, in zoom  
self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier)  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\clipper\mousemodes.py", line 168, in zoom  
self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier)  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\clipper\mousemodes.py", line 168, in zoom  
self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier)  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\clipper\mousemodes.py", line 168, in zoom  
self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier)  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\clipper\mousemodes.py", line 168, in zoom  
self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier)  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\clipper\mousemodes.py", line 168, in zoom  
self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier)  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\clipper\mousemodes.py", line 168, in zoom  
self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier)  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\clipper\mousemodes.py", line 168, in zoom  
self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier)  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\clipper\mousemodes.py", line 168, in zoom  
self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier)  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\clipper\mousemodes.py", line 168, in zoom  
self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier)  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\clipper\mousemodes.py", line 168, in zoom  
self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier)  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\clipper\mousemodes.py", line 168, in zoom  
self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier)  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\clipper\mousemodes.py", line 168, in zoom  
self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier)  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 457, in _wheel_event  
f.wheel(MouseEvent(event))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 389, in wheel  
self.zoom(100*d*psize, stereo_scaling = not event.alt_down())  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\site-
packages\chimerax\clipper\mousemodes.py", line 168, in zoom  
self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier)  
File "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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 "C:\Users\joel\AppData\Local\UCSF\ChimeraX\0.9\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: 3.3.0 NVIDIA 416.34
OpenGL renderer: GeForce GTX 1080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (4)

comment:1 by Tristan Croll, 6 years ago

Cc: Tristan Croll added
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 installed

This is another instance of #2214. Joel, the problem here is a bug in the ChimeraX ToolShed, causing it to ignore the ChimeraX version requirement when a bundle is automatically installed as a dependency. So when you install ISOLDE into ChimeraX 0.9, it fetches a version of Clipper built for the ChimeraX nightly builds (0.91) which fails due to API changes. The best remedy is to download a ChimeraX nightly and install ISOLDE into that (as well as fixing this issue, you'll get a bunch of other improvements and bug fixes into the bargain). Sorry for the hassle!

comment:2 by Tristan Croll, 6 years ago

Resolution: → duplicate
Status: assigned → closed

in reply to:  3 ; comment:3 by joel.mackay@…, 6 years ago 

Thanks for the response.
I see that there it a note on the ISOLDE web site that says that it doesn't work with chimeraX dailybuilds:
https://isolde.cimr.cam.ac.uk/download/
Are you saying that it *does* work with these?
Thanks very much
Joel


-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: Friday, 23 August 2019 7:04 PM
Cc: conrad@cgl.ucsf.edu; Joel Mackay <joel.mackay@sydney.edu.au>; tic20@cam.ac.uk
Subject: Re: [ChimeraX] #2347: Wrong version of Clipper installed (was: ChimeraX bug report submission)

#2347: Wrong version of Clipper installed
------------------------------------+--------------------------
          Reporter:  joel.mackay@…  |      Owner:  Conrad Huang
              Type:  defect         |     Status:  assigned
          Priority:  normal         |  Milestone:
         Component:  Tool Shed      |    Version:
        Resolution:                 |   Keywords:
        Blocked By:                 |   Blocking:
Notify when closed:                 |   Platform:  all
           Project:  ChimeraX       |
------------------------------------+--------------------------
Changes (by Tristan Croll):

 * status:  new => assigned
 * cc: Tristan Croll (added)
 * component:  Unassigned => Tool Shed
 * project:   => ChimeraX
 * platform:   => all
 * owner:  (none) => Conrad Huang


Comment:

 This is another instance of #2214. Joel, the problem here is a bug in the  ChimeraX ToolShed, causing it to ignore the ChimeraX version requirement  when a bundle is automatically installed as a dependency. So when you  install ISOLDE into ChimeraX 0.9, it fetches a version of Clipper built  for the ChimeraX nightly builds (0.91) which fails due to API changes. The  best remedy is to download a ChimeraX nightly and install ISOLDE into that  (as well as fixing this issue, you'll get a bunch of other improvements  and bug fixes into the bargain). Sorry for the hassle!

--
Ticket URL: <https://protect-au.mimecast.com/s/_Vc2CGvmB5iRlBKPSKsMJI?domain=plato.cgl.ucsf.edu>
ChimeraX <https://protect-au.mimecast.com/s/FRc2CJyp0qhvzB32HGxHoQ?domain=rbvi.ucsf.edu>
ChimeraX Issue Tracker

in reply to:  4 ; comment:4 by Tristan Croll, 6 years ago 

Argh! Thanks for pointing that out. I started releasing incremental 
development builds about 2 months back and announced it on the bulletin 
boards, but forgot to update the website. Each dev build is made to work 
with the ChimeraX daily build on the day of release. While there will be 
occasional times when something new in ChimeraX breaks compatibility, 
I'll usually have a new build in place fairly quickly in response.

On 2019-08-23 13:34, ChimeraX wrote:
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