Opened 7 years ago

Closed 7 years ago

Last modified 7 years ago

#1349 closed defect (fixed)

error reading pseudobond file

Reported by: Elaine Meng Owned by: Tom Goddard
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.7 (2018-08-07)
Description
error reading pseudobond file

pseudobond file attached (need to open PDB 5ego first) ... actually I was running the script in my struts feature highlight, struts.cxc
http://www.rbvi.ucsf.edu/chimerax/feature_highlights/struts.cxc


Log:
UCSF ChimeraX version: 0.7 (2018-08-07)  
OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102  
OpenGL renderer: NVIDIA GeForce GTX 675MX OpenGL Engine  
OpenGL vendor: NVIDIA Corporation  
How to cite UCSF ChimeraX  

open struts.cxc

open 5ego

Summary of feedback from opening 5ego fetched from pdb  
---  
notes | Fetching compressed mmCIF 5ego from
http://files.rcsb.org/download/5ego.cif  
Used PDBx fixed column width tables to speed up reading mmCIF file  
Used PDBx keywords to speed up reading mmCIF file  
  
Chain information for 5ego #1  
---  
Chain | Description  
A | Homeobox protein Meis1  
B | Homeobox protein Hox-B13  
D | DNA (5'-D(P*gp*tp*tp*gp*ap*cp*ap*gp*tp*tp*tp*tp*ap*(5CM)P*gp*ap*gp*G)-3')  
E | DNA (5'-D(*cp*cp*tp*(5CM)P*gp*tp*ap*ap*ap*ap*cp*tp*gp*tp*cp*ap*ap*C)-3')  
  

5ego citation:    Yin, Y., Morgunova, E., Jolma, A., Kaasinen, E., Sahu, B.,
Khund-Sayeed, S., Das, P.K., Kivioja, T., Dave, K., Zhong, F., Nitta, K.R.,
Taipale, M., Popov, A., Ginno, P.A., Domcke, S., Yan, J., Schubeler, D.,
Vinson, C., Taipale, J. (2017). Impact of cytosine methylation on DNA binding
specificities of human transcription factors. Science, 356. PMID: 28473536.
DOI: 10.1126/science.aaj2239  
Opened mmCIF data containing 1770 atoms and 1857 bonds  

hide atoms

show @ca

show nucleic

cartoon protein

cartoon style sides 24

~cartoon nucleic

cartoon hide nucleic

color /a 90,90,30

color /b salmon

surface nucleic enclose nucleic probeRadius 1.1

color nucleic light sea green

open 5ego.pb

Traceback (most recent call last):  
  File
"/Applications/ChimeraX-0.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/cmd_line/tool.py", line 205, in execute  
    cmd.run(cmd_text)  
  File
"/Applications/ChimeraX-0.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2561, in run  
    result = ci.function(session, **kw_args)  
  File
"/Applications/ChimeraX-0.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/open.py", line 41, in open  
    from_database=from_database, ignore_cache=ignore_cache, **kw))  
  File
"/Applications/ChimeraX-0.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/open.py", line 111, in open  
    models = handle_unknown_kw(session.models.open, paths, format=format,
name=name, **kw)  
  File
"/Applications/ChimeraX-0.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/open.py", line 62, in handle_unknown_kw  
    return f(*args, **kw)  
  File
"/Applications/ChimeraX-0.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/models.py", line 511, in open  
    session, filenames, format=format, name=name, **kw)  
  File
"/Applications/ChimeraX-0.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/io.py", line 444, in open_multiple_data  
    models, status = open_data(session, fspec, format=format, name=name, **kw)  
  File
"/Applications/ChimeraX-0.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/io.py", line 402, in open_data  
    models, status = open_func(*args, **kw)  
  File
"/Applications/ChimeraX-0.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/scripting.py", line 115, in open_command_script  
    run(session, text)  
  File
"/Applications/ChimeraX-0.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/run.py", line 31, in run  
    results = command.run(text, log=log)  
  File
"/Applications/ChimeraX-0.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2561, in run  
    result = ci.function(session, **kw_args)  
  File
"/Applications/ChimeraX-0.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/open.py", line 41, in open  
    from_database=from_database, ignore_cache=ignore_cache, **kw))  
  File
"/Applications/ChimeraX-0.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/open.py", line 111, in open  
    models = handle_unknown_kw(session.models.open, paths, format=format,
name=name, **kw)  
  File
"/Applications/ChimeraX-0.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/open.py", line 62, in handle_unknown_kw  
    return f(*args, **kw)  
  File
"/Applications/ChimeraX-0.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/models.py", line 508, in open  
    session, filenames, format=format, name=name, **kw)  
  File
"/Applications/ChimeraX-0.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/io.py", line 444, in open_multiple_data  
    models, status = open_data(session, fspec, format=format, name=name, **kw)  
  File
"/Applications/ChimeraX-0.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/io.py", line 404, in open_data  
    models, status = open_func(*args, **kw)  
  File
"/Applications/ChimeraX-0.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/read_pbonds/__init__.py", line 23, in open_file  
    return readpbonds.read_pseudobond_file(session, stream, file_name)  
  File
"/Applications/ChimeraX-0.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/read_pbonds/readpbonds.py", line 27, in read_pseudobond_file  
    aspec1, aspec2 = line.decode('utf-8').split()[:2]  
AttributeError: 'str' object has no attribute 'decode'  
  

AttributeError: 'str' object has no attribute 'decode'  
  
File
"/Applications/ChimeraX-0.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/read_pbonds/readpbonds.py", line 27, in read_pseudobond_file  
aspec1, aspec2 = line.decode('utf-8').split()[:2]  
  
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: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102
OpenGL renderer: NVIDIA GeForce GTX 675MX OpenGL Engine
OpenGL vendor: NVIDIA Corporation
File attachment: 5ego.pb

5ego.pb

Attachments (1)

5ego.pb (354 bytes ) - added by Elaine Meng 7 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (4)

by Elaine Meng, 7 years ago

Attachment: 5ego.pb added

Added by email2trac

comment:1 by Eric Pettersen, 7 years ago

Component: UnassignedInput/Output
Owner: set to Tom Goddard
Platform: all
Project: ChimeraX
Status: newassigned
Summary: ChimeraX bug report submissionerror reading pseudobond file

comment:2 by Eric Pettersen, 7 years ago

Resolution: fixed
Status: assignedclosed

comment:3 by Tom Goddard, 7 years ago

This was fixed a couple weeks ago. But you are running an older August 7 ChimeraX.

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