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
Added by email2trac