Opened 2 years ago

Closed 2 years ago

#10020 closed defect (duplicate)

MemoryError opening mmCIF files

Reported by: doilin@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc: Eric Pettersen
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7E2Y format mmcif fromDatabase pdb

Traceback (most recent call last):  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line
320, in interceptRequest  
self._callback(info)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line
93, in _intercept  
return interceptor(request_info, *args)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line
353, in intercept  
chimerax_intercept(*args, view=view, session=session)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line
455, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 368, in
thread_safe  
func(*args, **kw)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line
446, in defer  
cxcmd(session, topic)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line
464, in cxcmd  
run(session, cmd)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\run.py", line
38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2897, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2897, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
154, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
464, in collated_open  
return remember_data_format()  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\mmcif\\__init__.py", line 97,
in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "src\mmcif.pyx", line 418, in chimerax.mmcif.mmcif.fetch_mmcif  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\manager.py",
line 198, in open_data  
return provider_open(self.session, [path], _return_status=True,  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
465, in collated_open  
return remember_data_format()  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\mmcif\\__init__.py", line 43,
in open  
return mmcif.open_mmcif(session, data, file_name, **kw)  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
MemoryError: not enough memory  
  
MemoryError: not enough memory  
  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
  
See log for complete Python traceback.  
  

> open 7E2Y format mmcif fromDatabase pdb

Traceback (most recent call last):  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line
320, in interceptRequest  
self._callback(info)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line
93, in _intercept  
return interceptor(request_info, *args)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line
353, in intercept  
chimerax_intercept(*args, view=view, session=session)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line
455, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 368, in
thread_safe  
func(*args, **kw)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line
446, in defer  
cxcmd(session, topic)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line
464, in cxcmd  
run(session, cmd)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\run.py", line
38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2897, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2897, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
154, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
464, in collated_open  
return remember_data_format()  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\mmcif\\__init__.py", line 97,
in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "src\mmcif.pyx", line 418, in chimerax.mmcif.mmcif.fetch_mmcif  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\manager.py",
line 198, in open_data  
return provider_open(self.session, [path], _return_status=True,  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
465, in collated_open  
return remember_data_format()  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\mmcif\\__init__.py", line 43,
in open  
return mmcif.open_mmcif(session, data, file_name, **kw)  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
MemoryError: not enough memory  
  
MemoryError: not enough memory  
  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
  
See log for complete Python traceback.  
  

> open 7E2Y format mmcif fromDatabase pdb

Traceback (most recent call last):  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line
320, in interceptRequest  
self._callback(info)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line
93, in _intercept  
return interceptor(request_info, *args)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line
353, in intercept  
chimerax_intercept(*args, view=view, session=session)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line
455, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 368, in
thread_safe  
func(*args, **kw)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line
446, in defer  
cxcmd(session, topic)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line
464, in cxcmd  
run(session, cmd)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\run.py", line
38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2897, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2897, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
154, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
464, in collated_open  
return remember_data_format()  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\mmcif\\__init__.py", line 97,
in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "src\mmcif.pyx", line 418, in chimerax.mmcif.mmcif.fetch_mmcif  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\manager.py",
line 198, in open_data  
return provider_open(self.session, [path], _return_status=True,  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
465, in collated_open  
return remember_data_format()  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\mmcif\\__init__.py", line 43,
in open  
return mmcif.open_mmcif(session, data, file_name, **kw)  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
MemoryError: not enough memory  
  
MemoryError: not enough memory  
  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
  
See log for complete Python traceback.  
  

> open 7E2Y format mmcif fromDatabase pdb

Traceback (most recent call last):  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line
320, in interceptRequest  
self._callback(info)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line
93, in _intercept  
return interceptor(request_info, *args)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line
353, in intercept  
chimerax_intercept(*args, view=view, session=session)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line
455, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 368, in
thread_safe  
func(*args, **kw)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line
446, in defer  
cxcmd(session, topic)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line
464, in cxcmd  
run(session, cmd)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\run.py", line
38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2897, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2897, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
154, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
464, in collated_open  
return remember_data_format()  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\mmcif\\__init__.py", line 97,
in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "src\mmcif.pyx", line 418, in chimerax.mmcif.mmcif.fetch_mmcif  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\manager.py",
line 198, in open_data  
return provider_open(self.session, [path], _return_status=True,  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
465, in collated_open  
return remember_data_format()  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\mmcif\\__init__.py", line 43,
in open  
return mmcif.open_mmcif(session, data, file_name, **kw)  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
MemoryError: not enough memory  
  
MemoryError: not enough memory  
  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
  
See log for complete Python traceback.  
  

> open 7E2Y format mmcif fromDatabase pdb

Traceback (most recent call last):  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line
320, in interceptRequest  
self._callback(info)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line
93, in _intercept  
return interceptor(request_info, *args)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line
353, in intercept  
chimerax_intercept(*args, view=view, session=session)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line
455, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 368, in
thread_safe  
func(*args, **kw)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line
446, in defer  
cxcmd(session, topic)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line
464, in cxcmd  
run(session, cmd)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\run.py", line
38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2897, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2897, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
154, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
464, in collated_open  
return remember_data_format()  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\mmcif\\__init__.py", line 97,
in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "src\mmcif.pyx", line 418, in chimerax.mmcif.mmcif.fetch_mmcif  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\manager.py",
line 198, in open_data  
return provider_open(self.session, [path], _return_status=True,  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
465, in collated_open  
return remember_data_format()  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\mmcif\\__init__.py", line 43,
in open  
return mmcif.open_mmcif(session, data, file_name, **kw)  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
MemoryError: not enough memory  
  
MemoryError: not enough memory  
  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
  
See log for complete Python traceback.  
  

> open 7E2Y format mmcif fromDatabase pdb

Traceback (most recent call last):  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line
320, in interceptRequest  
self._callback(info)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line
93, in _intercept  
return interceptor(request_info, *args)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line
353, in intercept  
chimerax_intercept(*args, view=view, session=session)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line
455, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 368, in
thread_safe  
func(*args, **kw)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line
446, in defer  
cxcmd(session, topic)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line
464, in cxcmd  
run(session, cmd)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\run.py", line
38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2897, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2897, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
154, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
464, in collated_open  
return remember_data_format()  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\mmcif\\__init__.py", line 97,
in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "src\mmcif.pyx", line 418, in chimerax.mmcif.mmcif.fetch_mmcif  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\manager.py",
line 198, in open_data  
return provider_open(self.session, [path], _return_status=True,  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
465, in collated_open  
return remember_data_format()  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\mmcif\\__init__.py", line 43,
in open  
return mmcif.open_mmcif(session, data, file_name, **kw)  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
MemoryError: not enough memory  
  
MemoryError: not enough memory  
  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
  
See log for complete Python traceback.  
  

> open 7E2Y

Traceback (most recent call last):  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\cmd_line\tool.py", line 319,
in execute  
cmd.run(cmd_text)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2897, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2897, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
154, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
464, in collated_open  
return remember_data_format()  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\mmcif\\__init__.py", line 97,
in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "src\mmcif.pyx", line 418, in chimerax.mmcif.mmcif.fetch_mmcif  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\manager.py",
line 198, in open_data  
return provider_open(self.session, [path], _return_status=True,  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
465, in collated_open  
return remember_data_format()  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\mmcif\\__init__.py", line 43,
in open  
return mmcif.open_mmcif(session, data, file_name, **kw)  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
MemoryError: not enough memory  
  
MemoryError: not enough memory  
  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
  
See log for complete Python traceback.  
  

> open 7E2Y

Traceback (most recent call last):  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\cmd_line\tool.py", line 319,
in execute  
cmd.run(cmd_text)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2897, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2897, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
154, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
464, in collated_open  
return remember_data_format()  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\mmcif\\__init__.py", line 97,
in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "src\mmcif.pyx", line 418, in chimerax.mmcif.mmcif.fetch_mmcif  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\manager.py",
line 198, in open_data  
return provider_open(self.session, [path], _return_status=True,  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
465, in collated_open  
return remember_data_format()  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "E:\ChimeraX\bin\lib\site-packages\chimerax\mmcif\\__init__.py", line 43,
in open  
return mmcif.open_mmcif(session, data, file_name, **kw)  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
MemoryError: not enough memory  
  
MemoryError: not enough memory  
  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 442.50
OpenGL renderer: GeForce MX250/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: zh_CN.cp936
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: LENOVO
Model: 81WM
OS: Microsoft Windows 11 家庭中文版 (Build 22621)
Memory: 8,347,639,808
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-1065G7 CPU @ 1.30GHz
OSLanguage: zh-CN

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    comtypes: 1.1.14
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pywin32: 305
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    WMI: 1.5.1
    zipp: 3.15.0

Change History (3)

comment:1 by Eric Pettersen, 2 years ago

Cc: Eric Pettersen added
Component: Unassigned → Input/Output
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → MemoryError opening mmCIF files

comment:2 by Eric Pettersen, 2 years ago

Status: assigned → feedback

Hi,

Thanks for reporting this problem. We haven't been able to reproduce it ourselves, but nevertheless we have made what we _believe_ is a fix for it and that fix is in the current daily build. If you could try the daily build and let us know if it solves the problem for you, we would greatly appreciate it.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:3 by Greg Couch, 2 years ago

Resolution: → duplicate
Status: feedback → closed

Duplicated of #8815.

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