Opened 9 years ago

Closed 9 years ago

#352 closed defect (fixed)

can't use "sel" surface in symmetry center spec

Reported by: Elaine Meng Owned by: Tom Goddard
Priority: minor Milestone:
Component: Volume Data Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

This is an obscure situation, so low priority. If I select a surface and give "sel" as the center specification for symmetry (say with molmap) there is a traceback. However, "sel" is OK if only atoms are selected, and it works fine to use the model spec of that surface instead of selecting it. Example:

open 4hhb
surface
select #1.1
molmap :hem 5 symmetry c3 center #1.1
...works fine, but:
molmap :hem 5 symmetry c3 center sel
...gives traceback:

Traceback (most recent call last):
File "/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/cmd_line/gui.py", line 167, in execute
cmd.run(cmd_text)
File "/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/cli.py", line 2167, in run
self._process_keyword_arguments(final, prev_annos)
File "/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/cli.py", line 2106, in _process_keyword_arguments
value, text = self._parse_arg(anno, text, session, final)
File "/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/cli.py", line 1868, in _parse_arg
value, replacement, rest = annotation.parse(text, session)
File "/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/cli.py", line 773, in parse
elif obj.bounds() is None:
File "/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/objects.py", line 129, in bounds
bm.append(copies_bounding_box(b, m.positions.mask(minst)))
AttributeError: 'Places' object has no attribute 'mask'

Change History (1)

comment:1 by Tom Goddard, 9 years ago

Resolution: fixed
Status: newclosed

Fixed.

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