Opened 8 years ago

Closed 8 years ago

#750 closed defect (fixed)

could not save dcd, at least for PDB entries opened with "coord true"

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

Description

I tried both NMR ensembles 1g1p and 1plx. Example

open 1g1p coord t
save ~/Desktop/1g1p.dcd

Traceback (most recent call last):
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/cmd_line/tool.py", line 178, in execute
cmd.run(cmd_text)
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/cli.py", line 2366, in run
result = ci.function(session, kw_args)
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/save.py", line 58, in save
fmt.export(session, filename, fmt.nicknames[0],
kw)
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/io.py", line 161, in export
result = self.export_func(*args, kw)
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/toolshed/info.py", line 298, in save_cb
return save_shim(*args,
kw)
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/toolshed/info.py", line 295, in save_shim
return _func(*args, kw)
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/md_crds/init.py", line 31, in save_file
models = [m for m in models if isinstance(m, Structure)]
TypeError: 'NoneType' object is not iterable

Change History (2)

in reply to:  1 ; comment:1 by goddard@…, 8 years ago

The save command requires a models option when using DCD format.  Need to fix the code so it tells you that argument is required.

comment:2 by Tom Goddard, 8 years ago

Resolution: fixed
Status: assignedclosed

Fixed.

I made specifying models in the save dcd command optional -- if unspecified it uses all open structures.

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