![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 years ago
Closed 6 years ago
#2214 closed defect (fixed)
Incorrect version of Clipper installed in ChimeraX 0.9
| Reported by: | Owned by: | Conrad Huang | |
|---|---|---|---|
| Priority: | major | Milestone: | 0.92 |
| 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: Linux-4.15.0-54-generic-x86_64-with-debian-stretch-sid ChimeraX Version: 0.9 (2019-06-06) Description This happened when shift-scroll was used in ISODLE. According to isolde_intro.html: "When you zoom, the distance between the near and far clipping planes automatically grows and shrinks to provide depth cueing and reduce distracting clutter. If you need to adjust this, you can do so with shift-scroll." == ModuleNotFoundError: No module named 'chimerax.core.graphics.clipping' File "/usr/local/chimerax-0.9/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. Log: Startup Messages --- warning | 'clip' is a prefix of an existing command 'clipper' UCSF ChimeraX version: 0.9 (2019-06-06) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > toolshed show ISOLDE > set selectionWidth 4 before.pdb title: Crystal structure of etub from clostridium kluyveri [more info...] Chain information for before.pdb #1 --- Chain | Description A | predicted microcompartment protein Done loading forcefield before.pdb title: Crystal structure of etub from clostridium kluyveri [more info...] Chain information for before.pdb --- Chain | Description 1.3/A | predicted microcompartment protein WARNING: multiple experimental reflection datasets found: (dataset) FOBS, SIGFOBS, (dataset) IOBS, SIGIOBS, (dataset) DANO, SIGDANO, (dataset) F(+), SIGF(+), F(-), SIGF(-), (dataset) I(+), SIGI(+), I(-), SIGI(-) Automatically choosing "(dataset) IOBS, SIGIOBS". Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... > ~select #1 2 models selected > close #1 > open 1a0m structureFactors true Summary of feedback from opening 1a0m fetched from pdb --- warning | No free flags detected in this dataset! Automatically generated a new random set with 450 free from 9265 observed reflections. You should save your data to a new MTZ file and use this for any future rebuilding/refinement. notes | Fetching compressed mmCIF 1a0m from http://files.rcsb.org/download/1a0m.cif Fetching compressed 1a0m structure factors from http://files.rcsb.org/download/1a0m-sf.cif Resolution: 1.0944213038232693 1a0m title: 1.1 angstrom crystal structure of A-conotoxin [TYR15]-epi [more info...] Chain information for 1a0m --- Chain | Description 1.3/A 1.3/B | α-conotoxin [TYR15]-epi Non-standard residues in 1a0m #1.3 --- NH2 — amino group > hide #!1.2 models > show #!1.2 models > hide #!1.2 models Traceback (most recent call last): File "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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. > hide #!1.3.1 models > show #!1.3.1 models > hide #!1.3.2 models > show #!1.3.2 models > hide #!1.3.3 models > show #!1.3.3 models > hide #!1.3.3 models > show #!1.3.3 models > hide #!1.3.2 models > show #!1.3.2 models > hide #!1.3.2 models > show #!1.3.2 models > hide #!1.3.1 models > show #!1.3.1 models Traceback (most recent call last): File "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 65, in wheel z.far_clip_multiplier *= mult File "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 88, in far_clip_multiplier self.zoom(0) File "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 65, in wheel z.far_clip_multiplier *= mult File "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 88, in far_clip_multiplier self.zoom(0) File "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 65, in wheel z.far_clip_multiplier *= mult File "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 88, in far_clip_multiplier self.zoom(0) File "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/mouse_modes/mousemodes.py", line 457, in _wheel_event f.wheel(MouseEvent(event)) File "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 65, in wheel z.far_clip_multiplier *= mult File "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 88, in far_clip_multiplier self.zoom(0) File "/usr/local/chimerax-0.9/lib/python3.7/site- packages/chimerax/clipper/mousemodes.py", line 168, in zoom self.far_clip.plane_point = new_origin + distance*(1+self.far_clip_multiplier) File "/usr/local/chimerax-0.9/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 "/usr/local/chimerax-0.9/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: 3.3.0 NVIDIA 430.26 OpenGL renderer: GeForce GTX 1080 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation
Change History (10)
comment:1 by , 6 years ago
| Component: | Unassigned → Tool Shed |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Priority: | normal → major |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Incorrect version of Clipper installed in ChimeraX 0.9 |
comment:3 by , 6 years ago
I've had a second report of the same problem from a user installing ISOLDE into a fresh ChimeraX 0.9 installation.
comment:4 by , 6 years ago
Begin forwarded message:
From: Tristan Croll
Subject: Re: ChimeraX 0.91 release
Date: November 18, 2019 at 11:41:28 AM PST
To: Tom Goddard
Hi Tom,
... : all my versions of Clipper since 0.9.4 have had:
<Dependency name="ChimeraX-Core" version="==0.91"/>
... in the bundle_info.xml - this is clearly respected by the ToolShed when *manually* installing Clipper, but ignored when automatically installing it as a *dependency*. As far as I recall, there hasn't been any discussion of this one.
Tristan
comment:5 by , 6 years ago
| Milestone: | → 0.91 |
|---|
comment:6 by , 6 years ago
Using only empirical evidence and without delving into the bowels of pip, I think that pip:
- looks for the package to install and its dependencies
- if any dependency needs updating, download the latest version of the dependency
- repeat with newly downloaded dependencies
pip does, in fact, notice that the ISOLDE 1.0b3 and Clipper 0.9.11 require different versions of ChimeraX-Core, but it only logs the following message:
chimerax-clipper 0.9.11 has requirement ChimeraX-Core==0.91, but you'll have chimerax-core 0.9 which is incompatible.
without exiting with a non-zero status. And it installs both packages anyway.
4449ac0cf will make ChimeraX display warnings from pip, whether pip says the operation succeeded or not. Still need a way to avoid installing the wrong version of the bundle.
comment:7 by , 6 years ago
I'm reluctant to dig into (or worse, modify) pip, so here is a scheme that allows one to use the existing pip scheme and still have bundles that depend on particular ChimeraX releases.
First a description of the current situation:
To install ISOLDE, we must also install a compatible version of Clipper. And both ISOLDE and Clipper must also be compatible with the ChimeraX version being used. We currently have:
- For ChimeraX 0.9, Clipper 0.4.0 - 0.9.4, ISOLDE 1.0b3
- For ChimeraX 0.91, Clipper 0.9.5 - 0.9.11, ISOLDE 1.0b3.dev0 - 1.0b3.dev7
The dependency for ISOLDE 1.0b3 is Clipper>=0.9.4, which is certainly reasonable when 1.0b3 is released, since there could have been Clipper 0.9.5 and newer releases that are compatible with ChimeraX 0.9. The problem is, of course, ChimeraX 0.91 was released, and ISOLDE 1.0b3.dev0 and Clipper 0.9.5 were updated to be compatible with 0.91. So now the ISOLDE 1.0b3 dependency on Clipper>=0.9.4 can be satisfied (superficially) by the incompatible Clipper 0.9.5. Since pip always downloads the newest version of a package that satisfies the first level dependency, it installs Clipper 0.9.11 with ISOLDE 1.0b3; pip does detect the problem that the ChimeraX 0.9 dependency of Clipper 0.9.11 is not satisfied, but reports it as a warning rather than an error. But ChimeraX now has an unusable Clipper bundle installed and ISOLDE will not run.
Here's a proposal on how to work around the pip limitation:
Instead of using the >= operator (ISOLDE 1.0b3) to get newer versions of a bundle (Clipper 0.9.4) that is tied to a particular ChimeraX release (ChimeraX 0.9), we take advantage of pip always using the newest version of a package by using a wildcard in the version requirement. If we can rewrite history, we could have used these dependencies:
- For ChimeraX 0.9,
ISOLDE 1.0b3and1.0b3.dev*depend onClipper==0.9.*;Clipper 0.9.*depend onChimeraX-Core==0.9. - When ChimeraX 0.91 is released, ISOLDE and Clipper versions get advanced to
1.0b4and0.91.1, respectively.ISOLDE 1.0b4and1.0b4.dev*will depend onClipper==0.91.*;Clipper 0.91.*depend onChimeraX-Core==0.91.
The Clipper==0.XXX.* dependency can technically be satisfied by any version of Clipper 0.XXX.YYY but pip always pick the newest version. So both ISOLDE and Clipper can advance their version numbers and new releases of ChimeraX should not affect installation on older versions of ChimeraX.
Comments?
follow-up: 8 comment:8 by , 6 years ago
Good to have an explanation for this one! OK - I can easily work with that. On 2019-11-27 03:22, ChimeraX wrote:
comment:10 by , 6 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Switched over to new scheme for tying bundles to specific ChimeraX releases.
Note:
See TracTickets
for help on using tickets.
This looks like a ToolShed bug - is it checking the ChimeraX version requirements when installing dependencies? The offending line here was changed in Clipper 0.9.5 in response to a change in the ChimeraX API (double-checked - I just downloaded the 0.9.4 wheel and inspected the code). Clipper 0.9.5 has a strict version requirement for ChimeraX==0.91 - so how did it end up being installed into ChimeraX 0.9?
To solve your problem for the time being, I'd recommend downloading the ChimeraX daily build and installing ISOLDE into that. This will pull the latest development versions of ISOLDE and Clipper.