EMDB fetch timeout

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 0.93 (2020-04-03)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | Your computer has Intel graphics driver 8682 with a known bug that
causes all Qt user interface panels to be blank. ChimeraX can partially fix
this but may make some panel titlebars and edges black. Hopefully newer Intel
graphics drivers will fix this.  
  
UCSF ChimeraX version: 0.93 (2020-04-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 5199 fromDatabase emdb

Summary of feedback from opening 5199 fetched from emdb  
---  
note | Fetching compressed map 5199 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-5199/map/emd_5199.map.gz  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 44, in open  
db_models, status = _fetch_from_database(session, db_id, db_name, db_format,
name, ignore_cache, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 153, in _fetch_from_database  
ignore_cache=ignore_cache, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\fetch.py",
line 438, in fetch_from_database  
models, status = df.fetch(session, id, format=format,
ignore_cache=ignore_cache, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\fetch.py",
line 501, in fetch  
return fetch(session, database_id, ignore_cache=ignore_cache, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\emdb_fetch.py", line 45, in fetch_emdb  
uncompress = True, ignore_cache=ignore_cache)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\fetch.py",
line 69, in fetch_file  
check_certificates=check_certificates, name=name, timeout=timeout)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\fetch.py",
line 164, in retrieve_url  
read_and_uncompress(response, f, name, content_length, logger)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\fetch.py",
line 187, in read_and_uncompress  
read_and_report_progress(file_in, cdata, name, content_length, logger,
chunk_size)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\fetch.py",
line 202, in read_and_report_progress  
bytes = file_in.read(chunk_size)  
File "C:\Program Files\ChimeraX\bin\lib\tempfile.py", line 481, in
func_wrapper  
return func(*args, **kwargs)  
File "C:\Program Files\ChimeraX\bin\lib\tempfile.py", line 481, in
func_wrapper  
return func(*args, **kwargs)  
File "C:\Program Files\ChimeraX\bin\lib\socket.py", line 589, in readinto  
return self._sock.recv_into(b)  
socket.timeout: timed out  
  
socket.timeout: timed out  
  
File "C:\Program Files\ChimeraX\bin\lib\socket.py", line 589, in readinto  
return self._sock.recv_into(b)  
  
See log for complete Python traceback.  
  

> open 5199 fromDatabase emdb

Summary of feedback from opening 5199 fetched from emdb  
---  
note | Fetching compressed map 5199 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-5199/map/emd_5199.map.gz  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 44, in open  
db_models, status = _fetch_from_database(session, db_id, db_name, db_format,
name, ignore_cache, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 153, in _fetch_from_database  
ignore_cache=ignore_cache, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\fetch.py",
line 438, in fetch_from_database  
models, status = df.fetch(session, id, format=format,
ignore_cache=ignore_cache, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\fetch.py",
line 501, in fetch  
return fetch(session, database_id, ignore_cache=ignore_cache, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\emdb_fetch.py", line 45, in fetch_emdb  
uncompress = True, ignore_cache=ignore_cache)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\fetch.py",
line 69, in fetch_file  
check_certificates=check_certificates, name=name, timeout=timeout)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\fetch.py",
line 164, in retrieve_url  
read_and_uncompress(response, f, name, content_length, logger)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\fetch.py",
line 187, in read_and_uncompress  
read_and_report_progress(file_in, cdata, name, content_length, logger,
chunk_size)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\fetch.py",
line 202, in read_and_report_progress  
bytes = file_in.read(chunk_size)  
File "C:\Program Files\ChimeraX\bin\lib\tempfile.py", line 481, in
func_wrapper  
return func(*args, **kwargs)  
File "C:\Program Files\ChimeraX\bin\lib\tempfile.py", line 481, in
func_wrapper  
return func(*args, **kwargs)  
File "C:\Program Files\ChimeraX\bin\lib\socket.py", line 589, in readinto  
return self._sock.recv_into(b)  
socket.timeout: timed out  
  
socket.timeout: timed out  
  
File "C:\Program Files\ChimeraX\bin\lib\socket.py", line 589, in readinto  
return self._sock.recv_into(b)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 27.20.100.8682
OpenGL renderer: Intel(R) Iris(R) Plus Graphics 640
OpenGL vendor: Intel
Manufacturer: Microsoft Corporation
Model: Surface Laptop
OS: Microsoft Windows 10 Pro (Build 19045)
Memory: 8,503,017,472
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i7-7660U CPU @ 2.50GHz"

[Tom Goddard]

ChimeraX 0.93, wow! Apparently the EMDB ftp site did not respond. Error seems clear enough. Could improve the error message if this was reported often.