Opened 7 years ago

Closed 7 years ago

Last modified 7 years ago

#1418 closed defect (not a bug)

Clipper incompatible with ChimeraX >= 0.7

Reported by: ricardojstorquato@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-4.15.0-36-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 0.7 (2018-08-07)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.7 (2018-08-07)  
OpenGL version: 3.3.0 NVIDIA 390.77  
OpenGL renderer: GeForce GTX 550 Ti/PCIe/SSE2  
OpenGL vendor: NVIDIA Corporation  
How to cite UCSF ChimeraX  

open
/home/ricardo/dock_files/dock_a2b1-tilipo33/relax_files/tilipo33_model4_0004.pdb

Summary of feedback from opening
/home/ricardo/dock_files/dock_a2b1-tilipo33/relax_files/tilipo33_model4_0004.pdb  
---  
warnings | Ignored bad PDB record found on line 2456  
# All scores below are weighted scores, not raw scores.  
  
Ignored bad PDB record found on line 2457  
#BEGIN_POSE_ENERGIES_TABLE tilipo33_model4_0004.pdb  
  
Ignored bad PDB record found on line 2458  
label fa_atr fa_rep fa_sol fa_intra_rep fa_elec pro_close hbond_sr_bb
hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 coordinate_constraint rama omega
fa_dun p_aa_pp yhh_planarity ref total  
  
Ignored bad PDB record found on line 2459  
weights 1 0.55 0.9375 0.005 0.875 1.25 1.17 1.17 1.17 1.1 1.25 0.5 0.25 0.625
0.7 0.4 0.625 1 NA  
  
Ignored bad PDB record found on line 2460  
pose -610.088 119.074 389.624 1.84832 -50.0482 4.41986 -11.232 -36.6533
-9.12956 -5.13363 0.05167 55.6435 9.0983 21.8441 185.54 -9.71928 0.01719
-7.27326 47.8841  
  
168 messages similar to the above omitted  
  
Opened PDB data containing 2454 atoms and 2478 bonds  
Chain information for tilipo33_model4_0004.pdb #1  
---  
Chain | Description  
| No description available  
  

show selAtoms surfaces

set bgColor gray

set bgColor black

set bgColor white

set bgColor gray

set bgColor black

style selAtoms stick

Changed 2454 atom styles  

ui mousemode rightMode select

ui mousemode rightMode translate selected models

hide selAtoms

show selAtoms

hide selAtoms ribbons

hbonds selAtoms

101 hydrogen bonds found  

set bgColor gray

set bgColor white

ui mousemode rightMode play map series

ui mousemode rightMode tug

ui mousemode rightMode contour level

ui mousemode rightMode bond rotation

ui mousemode rightMode label

view cofr false

view cofr false

view orient cofr false

view orient cofr false

set bgColor black

lighting simple

lighting shadows true

lighting shadows false

lighting soft

lighting soft

lighting full

lighting flat

lighting flat

lighting full

toolshed show "Density Map Toolbar"

toolshed hide "Density Map Toolbar"

toolshed show "Density Map Toolbar"

volume selMaps style mesh

No volumes specified  

No volumes specified  

volume selMaps style surface

No volumes specified  

No volumes specified  

volume selMaps style solid

No volumes specified  

No volumes specified  

volume selMaps show

No volumes specified  

No volumes specified  

Downloading bundle ChimeraX_BlastProtein-0.1-py3-none-any.whl  
unloading module chimerax.blastprotein  
Successfully installed ChimeraX-BlastProtein-0.1  
No change in list of installed bundles  
Downloading bundle ChimeraX_Cytoscape-0.1-py3-none-any.whl  
Successfully installed ChimeraX-Cytoscape-0.1  
Installed ChimeraX-Cytoscape (0.1)  
Downloading bundle ChimeraX_SignalViewer-1.0-py3-none-any.whl  
Successfully installed ChimeraX-SignalViewer-1.0  
Installed ChimeraX-SignalViewer (1.0)  
Downloading bundle ChimeraX_Tempy-0.6.0-py3-none-any.whl  
Successfully installed ChimeraX-Tempy-0.6.0 biopython-1.72  
Installed ChimeraX-Tempy (0.6.0)  
Downloading bundle ChimeraX_Clipper-0.2.1-cp36-cp36m-linux_x86_64.whl  
Traceback (most recent call last):  
  File "/home/ricardo/chimerax/lib/python3.6/site-
packages/chimerax/ui/widgets/htmlview.py", line 366, in download_finished  
    session=self.session)  
  File "/home/ricardo/chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 548, in install_bundle  
    results = self._pip_install(bundle, per_user=per_user,
reinstall=reinstall)  
  File "/home/ricardo/chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 841, in _pip_install  
    results = self._run_pip(command)  
  File "/home/ricardo/chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 868, in _run_pip  
    raise RuntimeError(s)  
RuntimeError: Processing
./Downloads/ChimeraX_Clipper-0.2.1-cp36-cp36m-linux_x86_64.whl  
Collecting Clipper-Python>=0.1.1 (from ChimeraX-Clipper==0.2.1)  
  Downloading
https://files.pythonhosted.org/packages/43/84/e180c8bba9eb779cd46c809c66f5cd625d19d5bd3533160d19c7924af10a/Clipper_Python-0.1.1-cp36-cp36m-manylinux1_x86_64.whl
(31.1MB)  
Collecting ChimeraX-Core==0.6 (from ChimeraX-Clipper==0.2.1)  
  Could not find a version that satisfies the requirement ChimeraX-Core==0.6
(from ChimeraX-Clipper==0.2.1) (from versions: )  
No matching distribution found for ChimeraX-Core==0.6 (from ChimeraX-
Clipper==0.2.1)  
You are using pip version 9.0.3, however version 18.1 is available.  
You should consider upgrading via the 'pip install --upgrade pip' command.  
  
  

RuntimeError: Processing
./Downloads/ChimeraX_Clipper-0.2.1-cp36-cp36m-linux_x86_64.whl  
Collecting Clipper-Python>=0.1.1 (from ChimeraX-Clipper==0.2.1)  
Downloading
https://files.pythonhosted.org/packages/43/84/e180c8bba9eb779cd46c809c66f5cd625d19d5bd3533160d19c7924af10a/Clipper_Python-0.1.1-cp36-cp36m-manylinux1_x86_64.whl
(31.1MB)  
Collecting ChimeraX-Core==0.6 (from ChimeraX-Clipper==0.2.1)  
Could not find a version that satisfies the requirement ChimeraX-Core==0.6
(from ChimeraX-Clipper==0.2.1) (from versions: )  
No matching distribution found for ChimeraX-Core==0.6 (from ChimeraX-
Clipper==0.2.1)  
You are using pip version 9.0.3, however version 18.1 is available.  
You should consider upgrading via the 'pip install --upgrade pip' command.  
  
  
File "/home/ricardo/chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 868, in _run_pip  
raise RuntimeError(s)  
  
See log for complete Python traceback.  
  
If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu and
describe what you were doing and include a copy of the contents of the log.
Don't include any data you wish to remain private since a publicly viewable
bug report will be created.  

Downloading bundle ChimeraX_Clipper-0.2.1-cp36-cp36m-linux_x86_64.whl  
Traceback (most recent call last):  
  File "/home/ricardo/chimerax/lib/python3.6/site-
packages/chimerax/ui/widgets/htmlview.py", line 366, in download_finished  
    session=self.session)  
  File "/home/ricardo/chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 548, in install_bundle  
    results = self._pip_install(bundle, per_user=per_user,
reinstall=reinstall)  
  File "/home/ricardo/chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 841, in _pip_install  
    results = self._run_pip(command)  
  File "/home/ricardo/chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 868, in _run_pip  
    raise RuntimeError(s)  
RuntimeError: Processing
./Downloads/ChimeraX_Clipper-0.2.1-cp36-cp36m-linux_x86_64.whl  
Collecting ChimeraX-Core==0.6 (from ChimeraX-Clipper==0.2.1)  
  Could not find a version that satisfies the requirement ChimeraX-Core==0.6
(from ChimeraX-Clipper==0.2.1) (from versions: )  
No matching distribution found for ChimeraX-Core==0.6 (from ChimeraX-
Clipper==0.2.1)  
You are using pip version 9.0.3, however version 18.1 is available.  
You should consider upgrading via the 'pip install --upgrade pip' command.  
  
  

RuntimeError: Processing
./Downloads/ChimeraX_Clipper-0.2.1-cp36-cp36m-linux_x86_64.whl  
Collecting ChimeraX-Core==0.6 (from ChimeraX-Clipper==0.2.1)  
Could not find a version that satisfies the requirement ChimeraX-Core==0.6
(from ChimeraX-Clipper==0.2.1) (from versions: )  
No matching distribution found for ChimeraX-Core==0.6 (from ChimeraX-
Clipper==0.2.1)  
You are using pip version 9.0.3, however version 18.1 is available.  
You should consider upgrading via the 'pip install --upgrade pip' command.  
  
  
File "/home/ricardo/chimerax/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 868, in _run_pip  
raise RuntimeError(s)  
  
See log for complete Python traceback.  
  
If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu and
describe what you were doing and include a copy of the contents of the log.
Don't include any data you wish to remain private since a publicly viewable
bug report will be created.  




OpenGL version: 3.3.0 NVIDIA 390.77
OpenGL renderer: GeForce GTX 550 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (4)

comment:1 by pett, 7 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Clipper incompatible with ChimeraX >= 0.7

comment:2 by pett, 7 years ago

Resolution: → not a bug
Status: assigned → closed

Hi Ricardo,

As of right now, Clipper only works with ChimeraX version 0.6. You have version 0.7. So you would have to install the older version if you wanted to use Clipper.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

in reply to:  3 ; comment:3 by ricardojstorquato@…, 7 years ago 

Cool, thanks!

Em seg, 5 de nov de 2018 16:24, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu
escreveu:

in reply to:  4 ; comment:4 by tic20@…, 7 years ago 

Not too long now... there will *definitely* be a Clipper release soon after ChimeraX 0.8 goes stable.

 
 
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
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