Error in Basic Actions restoring session: invalid atom specifier

[daniel.palma.i@…]

The following bug report has been submitted:
Platform:        Linux-5.4.6-2-MANJARO-x86_64-with-arch-Manjaro-Linux
ChimeraX Version: 0.91 (2019-12-23)
Description
Trying to open a ChimeraX Session. This session had multiple named selections, this apparently is related to the bug.

Log:
UCSF ChimeraX version: 0.91 (2019-12-23)  
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daniel.palma.i@ug.uchile.cl is subscribed to the ChimeraX announcements list  

> open /home/danpal/Unidad/08_nudos_genomica_test/images/1oy5A_3ky7A_bak.cxs

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "/home/danpal/programs/chimerax-0.91/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 153, in _parse_unquoted  
ast = parser.parse(text, "atom_specifier", semantics=semantics)  
File "/home/danpal/programs/chimerax-0.91/lib/python3.7/site-
packages/grako/contexts.py", line 206, in parse  
result = rule()  
File "/home/danpal/programs/chimerax-0.91/lib/python3.7/site-
packages/grako/contexts.py", line 59, in wrapper  
return self._call(rule, name, params, kwparams)  
File "/home/danpal/programs/chimerax-0.91/lib/python3.7/site-
packages/grako/contexts.py", line 458, in _call  
node, newpos, newstate = self._invoke_rule(rule, name, params, kwparams)  
File "/home/danpal/programs/chimerax-0.91/lib/python3.7/site-
packages/grako/contexts.py", line 497, in _invoke_rule  
rule(self)  
File "/home/danpal/programs/chimerax-0.91/lib/python3.7/site-
packages/chimerax/core/commands/_atomspec.py", line 105, in _atom_specifier_  
self._error('no available options')  
File "/home/danpal/programs/chimerax-0.91/lib/python3.7/site-
packages/grako/contexts.py", line 433, in _error  
item  
grako.exceptions.FailedParse: (1:1) no available options :  
loop2a|loop2b  
^  
atom_specifier  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/danpal/programs/chimerax-0.91/lib/python3.7/site-
packages/chimerax/basic_actions/cmd.py", line 24, in name  
ast, used, unused = AtomSpecArg.parse(text, session)  
File "/home/danpal/programs/chimerax-0.91/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 97, in parse  
return cls._parse_unquoted(text, session)  
File "/home/danpal/programs/chimerax-0.91/lib/python3.7/site-
packages/chimerax/core/commands/atomspec.py", line 162, in _parse_unquoted  
raise AnnotationError(message, offset=e.pos)  
chimerax.core.commands.cli.AnnotationError: invalid atom specifier  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/danpal/programs/chimerax-0.91/lib/python3.7/site-
packages/chimerax/core/session.py", line 653, in restore  
obj = sm.restore_snapshot(self, data)  
File "/home/danpal/programs/chimerax-0.91/lib/python3.7/site-
packages/chimerax/basic_actions/statemgr.py", line 63, in restore_snapshot  
cmd.name(session, name, value)  
File "/home/danpal/programs/chimerax-0.91/lib/python3.7/site-
packages/chimerax/basic_actions/cmd.py", line 28, in name  
raise UserError("\"%s\": %s" % (text, str(e)))  
chimerax.core.errors.UserError: "loop2a|loop2b": invalid atom specifier  
  
opened ChimeraX session  




OpenGL version: 4.5 (Core Profile) Mesa 19.3.1
OpenGL renderer: AMD RAVEN (DRM 3.35.0, 5.4.6-2-MANJARO, LLVM 9.0.0)
OpenGL vendor: X.Org

[Eric Pettersen]

Reported by Daniel Palma Igor

[Conrad Huang]

Can you please send me the session that is causing the problem? Thanks.

[daniel.palma.i@…]

Of course

On Sun, 12 Jan 2020 at 19:09, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

1oy5A_3ky7A_bak.cxs​

[daniel.palma.i@…]

Added by email2trac

[Conrad Huang]

Just an update:

The problem is that basic_actions is restoring the aliases in random order, and was restoring "loop2" before "loop2a" and "loop2b". The right solution is to order the aliases, but the details still need to be worked out.

[Conrad Huang]

Fixed in 8c604053a. Instead of ordering the name definitions when restoring sessions, just assume that they are valid (since they were successfully defined previously) and create the name without error checks.

Fix should be in the daily build tomorrow (1/14/2020)