Opened 5 years ago

Closed 5 years ago

#3798 closed defect (duplicate)

Volume Viewer: unexpected indentation

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

Description 

The following bug report has been submitted:
Platform:        Linux-3.10.0-1127.19.1.el7.x86_64-x86_64-with-centos-7.8.2003-Core
ChimeraX Version: 1.0rc202005150054 (2020-05-15 00:54:28 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.0rc202005150054 (2020-05-15)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /data/simone/Manuscripts/Nop1_Nop56_RNA/Revision/Nop1short_56NTD_refine_19.pdb

Summary of feedback from opening
/data/simone/Manuscripts/Nop1_Nop56_RNA/Revision/Nop1short_56NTD_refine_19.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Date 2019-07-22 Time 08:17:51 CEST +0200 (1563776271.81 s)  
  
Ignored bad PDB record found on line 2  
REMARK PHENIX refinement  
  
Ignored bad PDB record found on line 4  
REMARK ****************** INPUT FILES AND LABELS
******************************  
  
Ignored bad PDB record found on line 5  
REMARK Reflections:  
  
Ignored bad PDB record found on line 6  
REMARK file name :
/nero/plu11/Projects/NBSC/Simone/xray/20190709_DESY_P11/Nop1short_56NTD/P29_D4/autobuild/AutoBuild_run_10_/exptl_fobs_phases_freeR_flags.mtz  
  
66 messages similar to the above omitted  
  
Chain information for Nop1short_56NTD_refine_19.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> select /A:152

24 atoms, 23 bonds, 1 model selected  

> show sel atoms

> select clear

> select /B:12,13

30 atoms, 29 bonds, 1 model selected  

> show sel atoms

> select clear

> hbonds

1310 hydrogen bonds found  

> select /a:149

17 atoms, 16 bonds, 1 model selected  

> show sel atoms

> select clear

> select /a:150

22 atoms, 21 bonds, 1 model selected  

> show sel atoms

> select /a:160

11 atoms, 10 bonds, 1 model selected  

> select /B:160

21 atoms, 21 bonds, 1 model selected  

> show sel atoms

> select /B:73

15 atoms, 14 bonds, 1 model selected  

> show sel atoms

> select /A:143

15 atoms, 14 bonds, 1 model selected  

> show sel atoms

> select /B:37

17 atoms, 16 bonds, 1 model selected  

> select /B:37,41

31 atoms, 29 bonds, 1 model selected  

> show sel atoms

> select clear

> select /A:242

17 atoms, 16 bonds, 1 model selected  

> select /A:241

21 atoms, 21 bonds, 1 model selected  

> show sel atoms

> select clear

> select /A:183,157

39 atoms, 37 bonds, 1 model selected  

> show sel atoms

> select clear

> select /A:184,157

29 atoms, 27 bonds, 1 model selected  

> show sel atoms

> select clear

> select /A:183

22 atoms, 21 bonds, 1 model selected  

> hide sel atoms

> select clear

> select /A:135

24 atoms, 23 bonds, 1 model selected  

> select /B:135

19 atoms, 18 bonds, 1 model selected  

> show sel atoms

> select clear

> select /BA:244

Nothing selected  

> select /A:244

11 atoms, 10 bonds, 1 model selected  

> show sel atoms

> select clear

> open /data/simone/Manuscripts/Nop1_Nop56_RNA/Revision/6RXU/emd_10052.map

Traceback (most recent call last):  
File "/data/simone/chimerax/chimerax-1.0-rc-2020.05.15/lib/python3.7/site-
packages/chimerax/open_command/dialog.py", line 146, in _qt_safe  
if data_format is None else " format " +
StringArg.unparse(data_format.nicknames[0])))  
File "/data/simone/chimerax/chimerax-1.0-rc-2020.05.15/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/data/simone/chimerax/chimerax-1.0-rc-2020.05.15/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2849, in run  
result = ci.function(session, **kw_args)  
File "/data/simone/chimerax/chimerax-1.0-rc-2020.05.15/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 101, in cmd_open  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/data/simone/chimerax/chimerax-1.0-rc-2020.05.15/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2849, in run  
result = ci.function(session, **kw_args)  
File "/data/simone/chimerax/chimerax-1.0-rc-2020.05.15/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 152, in provider_open  
name or model_name_from_path(fi.file_name)), provider_kw)  
File "/data/simone/chimerax/chimerax-1.0-rc-2020.05.15/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 380, in collated_open  
return func(*func_args, **func_kw)  
File "/data/simone/chimerax/chimerax-1.0-rc-2020.05.15/lib/python3.7/site-
packages/chimerax/map/__init__.py", line 147, in open  
return open_map(session, path, format=_name, **kw)  
File "/data/simone/chimerax/chimerax-1.0-rc-2020.05.15/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3307, in open_map  
smodels, smsg = open_grids(session, sgrids, name, **kw)  
File "/data/simone/chimerax/chimerax-1.0-rc-2020.05.15/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3367, in open_grids  
show_volume_dialog(session)  
File "/data/simone/chimerax/chimerax-1.0-rc-2020.05.15/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3191, in show_volume_dialog  
from .volume_viewer import show_volume_dialog  
File "/data/simone/chimerax/chimerax-1.0-rc-2020.05.15/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 4955  
except Exception:  
^  
IndentationError: unexpected unindent  
  
File "/data/simone/chimerax/chimerax-1.0-rc-2020.05.15/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 4955  
except Exception:  
^  
IndentationError: unexpected unindent  
  
File "/data/simone/chimerax/chimerax-1.0-rc-2020.05.15/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3191, in show_volume_dialog  
from .volume_viewer import show_volume_dialog  
  
See log for complete Python traceback.  
  

> open /data/simone/Manuscripts/Nop1_Nop56_RNA/Revision/5WLC/emd_8859.map

Traceback (most recent call last):  
File "/data/simone/chimerax/chimerax-1.0-rc-2020.05.15/lib/python3.7/site-
packages/chimerax/open_command/dialog.py", line 146, in _qt_safe  
if data_format is None else " format " +
StringArg.unparse(data_format.nicknames[0])))  
File "/data/simone/chimerax/chimerax-1.0-rc-2020.05.15/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/data/simone/chimerax/chimerax-1.0-rc-2020.05.15/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2849, in run  
result = ci.function(session, **kw_args)  
File "/data/simone/chimerax/chimerax-1.0-rc-2020.05.15/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 101, in cmd_open  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/data/simone/chimerax/chimerax-1.0-rc-2020.05.15/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2849, in run  
result = ci.function(session, **kw_args)  
File "/data/simone/chimerax/chimerax-1.0-rc-2020.05.15/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 152, in provider_open  
name or model_name_from_path(fi.file_name)), provider_kw)  
File "/data/simone/chimerax/chimerax-1.0-rc-2020.05.15/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 380, in collated_open  
return func(*func_args, **func_kw)  
File "/data/simone/chimerax/chimerax-1.0-rc-2020.05.15/lib/python3.7/site-
packages/chimerax/map/__init__.py", line 147, in open  
return open_map(session, path, format=_name, **kw)  
File "/data/simone/chimerax/chimerax-1.0-rc-2020.05.15/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3307, in open_map  
smodels, smsg = open_grids(session, sgrids, name, **kw)  
File "/data/simone/chimerax/chimerax-1.0-rc-2020.05.15/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3367, in open_grids  
show_volume_dialog(session)  
File "/data/simone/chimerax/chimerax-1.0-rc-2020.05.15/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3191, in show_volume_dialog  
from .volume_viewer import show_volume_dialog  
File "/data/simone/chimerax/chimerax-1.0-rc-2020.05.15/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 4955  
except Exception:  
^  
IndentationError: unexpected unindent  
  
File "/data/simone/chimerax/chimerax-1.0-rc-2020.05.15/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 4955  
except Exception:  
^  
IndentationError: unexpected unindent  
  
File "/data/simone/chimerax/chimerax-1.0-rc-2020.05.15/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3191, in show_volume_dialog  
from .volume_viewer import show_volume_dialog  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 450.66
OpenGL renderer: Quadro K600/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: OptiPlex 9020
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 4 Intel(R) Core(TM) i5-4690 CPU @ 3.50GHz
Cache Size: 6144 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            15G         11G        2.4G        382M        1.5G        3.1G
	Swap:          7.8G         10M        7.8G

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GK107GL [Quadro K600] [10de:0ffa] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:094b]	
	Kernel driver in use: nvidia
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

Change History (2)

comment:1 by pett, 5 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Volume Viewer: unexpected indentation

comment:2 by Tom Goddard, 5 years ago

Resolution: → duplicate
Status: assigned → closed

Fixed 4 months ago.

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