Opened 3 years ago

Closed 3 years ago

#7869 closed defect (duplicate)

Problem fetching mmCIF template: URL can't contain control characters

Reported by: chimerax-bug-report@… Owned by: Greg Couch
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:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3.dev202110261153 (2021-10-26 11:53:52 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3.dev202110261153 (2021-10-26)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Volumes/groups/ameres/Annamaria/alpha_fold/2021-10-31_2to2_Dis3l2_Tailor/prediction_Dis3l2_1235Tailor_1180_8905f/rank_5_model_4_ptm_seed_0_unrelaxed.pdb

Chain information for rank_5_model_4_ptm_seed_0_unrelaxed.pdb #1  
---  
Chain | Description  
A B | No description available  
C D | No description available  
  

> show cartoons

> show atoms

[Repeated 1 time(s)]

> hide atoms

> color bychain

> open
> /Volumes/groups/ameres/Annamaria/alpha_fold/2021-11-02_Tailor_Dis3l2_FL/prediction_ComplexTailorFL_Dis3l2FL_5994b/rank_1_model_3_ptm_seed_0_unrelaxed.pdb

Chain information for rank_1_model_3_ptm_seed_0_unrelaxed.pdb #2  
---  
Chain | Description  
A B | No description available  
C | No description available  
  

> hide #1 models

> color #2 bychain

> color #2 byhetero

[Repeated 1 time(s)]

> color #2 bychain

[Repeated 1 time(s)]

> coulombic #2

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for rank_1_model_3_ptm_seed_0_unrelaxed.pdb_A SES surface
#2.1: minimum, -19.58, mean 1.10, maximum 20.80  
Coulombic values for rank_1_model_3_ptm_seed_0_unrelaxed.pdb_B SES surface
#2.2: minimum, -19.61, mean 0.76, maximum 16.39  
Coulombic values for rank_1_model_3_ptm_seed_0_unrelaxed.pdb_C SES surface
#2.3: minimum, -21.20, mean -0.24, maximum 23.66  
To also show corresponding color key, enter the above coulombic command and
add key true  

> undo

[Repeated 2 time(s)]

> color #!2 bychain

> show #!2 cartoons

> open
> /Volumes/groups/ameres/Annamaria/alpha_fold/prediction_Dis3l2Tailor_7d197/rank_1_model_1_ptm_seed_0_unrelaxed.pdb

Chain information for rank_1_model_1_ptm_seed_0_unrelaxed.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #!2 models

> show #!2 models

> hide #3 models

> hide #!2 surfaces

> show #!2 surfaces

> hide #!2 surfaces

> show #!2 surfaces

> hide #!2 surfaces

> hide #!2 atoms

> hide #!2 cartoons

[Repeated 1 time(s)]

> show #!2 cartoons

> rainbow #!2

[Repeated 1 time(s)]

> undo

[Repeated 1 time(s)]

> show #1 models

> hide #!2 models

> close #2

> show #3 models

> hide #1 models

> close #1

> close

> open
> /Volumes/vbc/BCHMCB/B/AMERES/Annamaria/alphafold/Falk_DIS3L2_Tailor_39353.result/DIS3L2_Tailor_39353_unrelaxed_rank_1_model_5.pdb

Chain information for DIS3L2_Tailor_39353_unrelaxed_rank_1_model_5.pdb #1  
---  
Chain | Description  
B | No description available  
C | No description available  
  

> color bychain

[Repeated 1 time(s)]

> show surfaces

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for DIS3L2_Tailor_39353_unrelaxed_rank_1_model_5.pdb_B SES
surface #1.1: minimum, -40.03, mean -0.09, maximum 22.28  
Coulombic values for DIS3L2_Tailor_39353_unrelaxed_rank_1_model_5.pdb_C SES
surface #1.2: minimum, -19.38, mean 1.02, maximum 16.13  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide #1.1 models

> show #1.1 models

> hide #1.2 models

> hide #1.1 models

> show #1.2 models

> undo

> show #1.1 models

> hide #1.1 models

> show #1.2 models

> hide #1.2 models

> show #1.1 models

> hide #1.1 models

> show #1.2 models

> save "/Users/annamaria.sgromo/Documents/model Tailor and Dis3l2_Surface
> Tailor_1to1.png" width 864 height 604 supersample 3

> show #1.1 models

> hide #1.1 models

> hide #1.2 models

> show #1.1 models

> save "/Users/annamaria.sgromo/Documents/model Tailor and Dis3l2_Surface
> Dis3l2_1to1.png" width 864 height 604 supersample 3

> show #1.2 models

> hide #1.1 models

> mlp

Map values for surface "DIS3L2_Tailor_39353_unrelaxed_rank_1_model_5.pdb_B SES
surface": minimum -30.21, mean -4.991, maximum 24.63  
Map values for surface "DIS3L2_Tailor_39353_unrelaxed_rank_1_model_5.pdb_C SES
surface": minimum -27.98, mean -4.08, maximum 25.19  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide #1.2 models

> show #1.2 models

> hide #1.1 models

> show #1.1 models

> hide #1.2 models

> select #1.1

8206 atoms, 1032 residues, 1 model selected  

> ~select #1.1

1 model selected  

> show #1.2 models

> hide #1.2 target m

> hide #!1 models

> hide #1.1 models

> show #1.1 models

> select #1.1

8206 atoms, 1032 residues, 1 model selected  

> hide sel surfaces

> volume style surface

No volumes specified  

> transparency sel 50

> ~select #1.1

1 model selected  

> hide #1.1 models

> show #1.1 models

> transparency #1.1 0

> color bychain

> mlp

Map values for surface "DIS3L2_Tailor_39353_unrelaxed_rank_1_model_5.pdb_B SES
surface": minimum -30.21, mean -4.991, maximum 24.63  
Map values for surface "DIS3L2_Tailor_39353_unrelaxed_rank_1_model_5.pdb_C SES
surface": minimum -27.98, mean -4.08, maximum 25.19  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide #1.1 models

> show #1.1 models

> transparency 0

> transparency 50

> transparency 0

> transparency 50

> transparency 0

> volume style image

No volumes specified  

> transparency 50

> hide #1.2 models

> show #1.2 models

> transparency 0

> hide #1.1 models

> show #1.1 models

> hide #1.2 models

> transparency #1.1 50

> show #1.2 models

> hide #1.1 models

> show #1.1 models

> hide #1.2 models

> coulombic

Coulombic values for DIS3L2_Tailor_39353_unrelaxed_rank_1_model_5.pdb_B SES
surface #1.1: minimum, -40.03, mean -0.09, maximum 22.28  
Coulombic values for DIS3L2_Tailor_39353_unrelaxed_rank_1_model_5.pdb_C SES
surface #1.2: minimum, -19.38, mean 1.02, maximum 16.13  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide #1.1 models

> hide #1.2 models

> show #1.2 models

> show #1.1 models

> hide #1.1 models

> hide #1.2 models

> show #1.1 models

> show #1.2 models

> hide #1.1 models

> show #1.1 models

> hide #1.2 models

> show #1.2 models

> hide #1.1 models

> show #1.1 models

> hide #1.2 models

> open /Users/annamaria.sgromo/Downloads/5Z4C.cif

Traceback (most recent call last):  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/graphics.py", line 51, in event  
if self.handle_drag_and_drop(event):  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/graphics.py", line 116, in handle_drag_and_drop  
mw.dropEvent(event)  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 588, in dropEvent  
_open_dropped_file(self.session, p)  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1931, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 457, in collated_open  
return remember_data_format()  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mmcif/__init__.py", line 40, in open  
return mmcif.open_mmcif(session, data, file_name, **kw)  
File "src/mmcif.pyx", line 82, in chimerax.mmcif.mmcif.open_mmcif  
File "src/mmcif.pyx", line 68, in chimerax.mmcif.mmcif._initialize.lambda  
File "src/mmcif.pyx", line 373, in chimerax.mmcif.mmcif._get_template  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/fetch.py", line 88, in fetch_file  
retrieve_url(url, filename, uncompress=uncompress,
transmit_compressed=transmit_compressed,  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/fetch.py", line 181, in retrieve_url  
with urlopen(request, timeout=timeout, context=ssl_context) as response:  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/urllib/request.py",
line 214, in urlopen  
return opener.open(url, data, timeout)  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/urllib/request.py",
line 517, in open  
response = self._open(req, data)  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/urllib/request.py",
line 534, in _open  
result = self._call_chain(self.handle_open, protocol, protocol +  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/urllib/request.py",
line 494, in _call_chain  
result = func(*args)  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/urllib/request.py",
line 1375, in http_open  
return self.do_open(http.client.HTTPConnection, req)  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/urllib/request.py",
line 1346, in do_open  
h.request(req.get_method(), req.selector, req.data, headers,  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py",
line 1257, in request  
self._send_request(method, url, body, headers, encode_chunked)  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py",
line 1268, in _send_request  
self.putrequest(method, url, **skips)  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py",
line 1102, in putrequest  
self._validate_path(url)  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py",
line 1202, in _validate_path  
raise InvalidURL(f"URL can't contain control characters. {url!r} "  
http.client.InvalidURL: URL can't contain control characters. '/reports/ /
MET/ MET.cif' (found at least ' ')  
  
http.client.InvalidURL: URL can't contain control characters. '/reports/ /
MET/ MET.cif' (found at least ' ')  
  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py",
line 1202, in _validate_path  
raise InvalidURL(f"URL can't contain control characters. {url!r} "  
  
See log for complete Python traceback.  
  

> open /Users/annamaria.sgromo/Downloads/5Z4C.cif

Traceback (most recent call last):  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 282, in event  
_open_dropped_file(self.session, event.file())  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1931, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 457, in collated_open  
return remember_data_format()  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mmcif/__init__.py", line 40, in open  
return mmcif.open_mmcif(session, data, file_name, **kw)  
File "src/mmcif.pyx", line 82, in chimerax.mmcif.mmcif.open_mmcif  
File "src/mmcif.pyx", line 68, in chimerax.mmcif.mmcif._initialize.lambda  
File "src/mmcif.pyx", line 373, in chimerax.mmcif.mmcif._get_template  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/fetch.py", line 88, in fetch_file  
retrieve_url(url, filename, uncompress=uncompress,
transmit_compressed=transmit_compressed,  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/fetch.py", line 181, in retrieve_url  
with urlopen(request, timeout=timeout, context=ssl_context) as response:  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/urllib/request.py",
line 214, in urlopen  
return opener.open(url, data, timeout)  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/urllib/request.py",
line 517, in open  
response = self._open(req, data)  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/urllib/request.py",
line 534, in _open  
result = self._call_chain(self.handle_open, protocol, protocol +  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/urllib/request.py",
line 494, in _call_chain  
result = func(*args)  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/urllib/request.py",
line 1375, in http_open  
return self.do_open(http.client.HTTPConnection, req)  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/urllib/request.py",
line 1346, in do_open  
h.request(req.get_method(), req.selector, req.data, headers,  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py",
line 1257, in request  
self._send_request(method, url, body, headers, encode_chunked)  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py",
line 1268, in _send_request  
self.putrequest(method, url, **skips)  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py",
line 1102, in putrequest  
self._validate_path(url)  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py",
line 1202, in _validate_path  
raise InvalidURL(f"URL can't contain control characters. {url!r} "  
http.client.InvalidURL: URL can't contain control characters. '/reports/ /
MET/ MET.cif' (found at least ' ')  
  
http.client.InvalidURL: URL can't contain control characters. '/reports/ /
MET/ MET.cif' (found at least ' ')  
  
File
"/private/var/folders/vc/sf8_qgq95nb557qn9rkq15m4001sks/T/AppTranslocation/ADCE71BE-B2AD-4882-91E0-D972B74C9686/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py",
line 1202, in _validate_path  
raise InvalidURL(f"URL can't contain control characters. {url!r} "  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-16.5.14
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro14,1
      Processor Name: Dual-Core Intel Core i7
      Processor Speed: 2.5 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 451.140.1.0.0
      SMC Version (system): 2.43f11

Software:

    System Software Overview:

      System Version: macOS 11.7 (20G817)
      Kernel Version: Darwin 20.6.0
      Time since boot: 29 days 23:38

Graphics/Displays:

    Intel Iris Plus Graphics 640:

      Chipset Model: Intel Iris Plus Graphics 640
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x5926
      Revision ID: 0x0006
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        HP ZR2440w:
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: CN423402JK  
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: Yes
          Connection Type: DVI or HDMI
          Adapter Firmware Version: 7.55

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.1
    charset-normalizer: 2.0.7
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.1.6
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202110261153
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.3
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.4
    ChimeraX-ModelPanel: 1.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.8
    ChimeraX-PDB: 2.6.4
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.5
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.6
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.10.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.5.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.8.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.7.3
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.2
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.21
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.1
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.2
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Input/Output
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Problem fetching mmCIF template: URL can't contain control characters

comment:2 by Eric Pettersen, 3 years ago

Resolution: → duplicate
Status: assigned → closed

duplicate of #6508

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