opening omap file gives IndentationError: unexpected unindent

[Elaine Meng]

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 1.0rc202005150054 (2020-05-15 00:54:28 UTC)
Description
I tried setting ChimeraX as the app to open all .omap files and then I double-clicked the .omap file in finder.  It was an old .omap file I had sitting around that opens fine in Chimera but I attach it just in case.

Log:
> open /Users/meng/Desktop/startup.cxc

> alias reset view orient; view initial

> alias start toolshed show $1

> alias whereprefs info path user unversioned config

> alias previewts toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu;toolshed reload available

> alias normalts toolshed url https://cxtoolshed.rbvi.ucsf.edu;toolshed reload
> available

> alias btut open
> http://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/tutorials/binding-
> sites.html

> alias segtest open 0557 from emdb; vol threshold #1 min 0; vol scale #2
> value uint8; open 6nzk

executed startup.cxc  
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 /Users/meng/Desktop/stash/1tkkA.pdb

Summary of feedback from opening /Users/meng/Desktop/stash/1tkkA.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 16 16 SER B
58 VAL B 69 1 12  
Start residue of secondary structure not found: HELIX 17 17 LEU B 70 LEU B 75
1 6  
Start residue of secondary structure not found: HELIX 18 18 SER B 78 ALA B 80
5 3  
Start residue of secondary structure not found: HELIX 19 19 GLY B 81 LEU B 92
1 12  
Start residue of secondary structure not found: HELIX 20 20 ASN B 96 CYS B 115
1 20  
213 messages similar to the above omitted  
Cannot find LINK/SSBOND residue ALA (2478 )  
Cannot find LINK/SSBOND residue ALA (2474 )  
Cannot find LINK/SSBOND residue ALA (2482 )  
Cannot find LINK/SSBOND residue ALA (2476 )  
Cannot find LINK/SSBOND residue ALA (2472 )  
38 messages similar to the above omitted  
  
1tkkA.pdb title:  
The structure of A substrate-liganded complex of the L-ala- D/L-glu epimerase
from bacillus subtilis [more info...]  
  
Chain information for 1tkkA.pdb #1  
---  
Chain | Description  
A | similar to chloromuconate cycloisomerase  
  
Non-standard residues in 1tkkA.pdb #1  
---  
MG — magnesium ion  
  

> open /Users/meng/Desktop/stash/1tkkA.pdb

Summary of feedback from opening /Users/meng/Desktop/stash/1tkkA.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 16 16 SER B
58 VAL B 69 1 12  
Start residue of secondary structure not found: HELIX 17 17 LEU B 70 LEU B 75
1 6  
Start residue of secondary structure not found: HELIX 18 18 SER B 78 ALA B 80
5 3  
Start residue of secondary structure not found: HELIX 19 19 GLY B 81 LEU B 92
1 12  
Start residue of secondary structure not found: HELIX 20 20 ASN B 96 CYS B 115
1 20  
213 messages similar to the above omitted  
Cannot find LINK/SSBOND residue ALA (2478 )  
Cannot find LINK/SSBOND residue ALA (2474 )  
Cannot find LINK/SSBOND residue ALA (2482 )  
Cannot find LINK/SSBOND residue ALA (2476 )  
Cannot find LINK/SSBOND residue ALA (2472 )  
38 messages similar to the above omitted  
  
1tkkA.pdb title:  
The structure of A substrate-liganded complex of the L-ala- D/L-glu epimerase
from bacillus subtilis [more info...]  
  
Chain information for 1tkkA.pdb #2  
---  
Chain | Description  
A | similar to chloromuconate cycloisomerase  
  
Non-standard residues in 1tkkA.pdb #2  
---  
MG — magnesium ion  
  

> open /Users/meng/Desktop/stash/2fma.omap

Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX-1.0-rc-2020.05.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 238, in event  
_open_dropped_file(self.session, event.file())  
File
"/Users/meng/Desktop/ChimeraX-1.0-rc-2020.05.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1724, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File
"/Users/meng/Desktop/ChimeraX-1.0-rc-2020.05.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Users/meng/Desktop/ChimeraX-1.0-rc-2020.05.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2849, in run  
result = ci.function(session, **kw_args)  
File
"/Users/meng/Desktop/ChimeraX-1.0-rc-2020.05.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Users/meng/Desktop/ChimeraX-1.0-rc-2020.05.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2849, in run  
result = ci.function(session, **kw_args)  
File
"/Users/meng/Desktop/ChimeraX-1.0-rc-2020.05.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Users/meng/Desktop/ChimeraX-1.0-rc-2020.05.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 380, in collated_open  
return func(*func_args, **func_kw)  
File
"/Users/meng/Desktop/ChimeraX-1.0-rc-2020.05.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/__init__.py", line 147, in open  
return open_map(session, path, format=_name, **kw)  
File
"/Users/meng/Desktop/ChimeraX-1.0-rc-2020.05.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3307, in open_map  
smodels, smsg = open_grids(session, sgrids, name, **kw)  
File
"/Users/meng/Desktop/ChimeraX-1.0-rc-2020.05.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3367, in open_grids  
show_volume_dialog(session)  
File
"/Users/meng/Desktop/ChimeraX-1.0-rc-2020.05.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3191, in show_volume_dialog  
from .volume_viewer import show_volume_dialog  
File
"/Users/meng/Desktop/ChimeraX-1.0-rc-2020.05.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 4955  
except Exception:  
^  
IndentationError: unexpected unindent  
  
File
"/Users/meng/Desktop/ChimeraX-1.0-rc-2020.05.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume_viewer.py", line 4955  
except Exception:  
^  
IndentationError: unexpected unindent  
  
File
"/Users/meng/Desktop/ChimeraX-1.0-rc-2020.05.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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: 4.1 INTEL-12.10.17
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro11,4
      Processor Name: Intel Core i7
      Processor Speed: 2.2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 197.0.0.0.0
      SMC Version (system): 2.29f24

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G4032)
      Kernel Version: Darwin 18.7.0
      Time since boot: 1:25

Graphics/Displays:

    Intel Iris Pro:

      Chipset Model: Intel Iris Pro
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x0d26
      Revision ID: 0x0008
      Metal: Supported, feature set macOS GPUFamily1 v4
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8
File attachment: 2fma.omap

2fma.omap​

[Elaine Meng]

Added by email2trac

[Tom Goddard]

Greg misindented the volume code but fixed in a few days ago. Should be fixed in current ChimeraX builds on download page.