opening 4b3o can produce KeyError generating chain descriptions

[Greg Couch]

The following bug report has been submitted:
Platform:        Windows-10-10.0.17134
ChimeraX Version: 0.7 (2018-07-26)
Description
open 4b3o; close; open 4b30 format pdb

Opening in the other order is fine

Log:
UCSF ChimeraX version: 0.7 (2018-07-26)  
OpenGL version: 3.3.0 NVIDIA 391.24  
OpenGL renderer: GeForce GTX 970/PCIe/SSE2  
OpenGL vendor: NVIDIA Corporation  
How to cite UCSF ChimeraX  

open 4b3o

Summary of feedback from opening 4b3o fetched from pdb  
---  
warning | Expected gap or linking atom in U #18 for C #17 in chain R  
notes | Used PDBx fixed column width tables to speed up reading mmCIF file  
Used PDBx keywords to speed up reading mmCIF file  
  
Chain information for 4b3o #1  
---  
Chain | Description  
A | reverse transcriptase/ribonuclease H  
B | P51 rt  
D | 5'-D(*cp*gp*tp*ap*tp*gp*cp*cp*tp*ap*tp*ap*gp*tp
*tp*ap*tp*tp*gp*tp*gp*gp*cp*C)-3'  
R | 5'-R(*ap*up*gp*ap*3DRP*gp*gp*cp*cp*ap*cp*ap*ap*up*ap
*ap*cp*up*ap*up*ap*gp*gp*cp*ap*up*A)-3'  
  

4b3o citation:    Lapkouski, M., Tian, L., Miller, J.T., Le Grice, S.F.J.,
Yang, W. (2013). Complexes of HIV-1 RT, Nnrti and RNA/DNA Hybrid Reveal a
Structure Compatible with RNA Degradation. Nat.Struct.Mol.Biol., 20, 230.
PMID: 23314251. DOI: 10.1038/NSMB.2485  
Opened mmCIF data containing 8513 atoms and 8823 bonds  

close

open 4b3o format PDB

Summary of feedback from opening 4b3o fetched from pdb  
---  
warning | Residues corresponding to PDB SEQRES record for chain D are missing.
Ignoring record as basis for sequence.  
  
Traceback (most recent call last):  
  File "C:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 205, in execute  
    cmd.run(cmd_text)  
  File "C:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2561, in run  
    result = ci.function(session, **kw_args)  
  File "C:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\core\commands\open.py", line 41, in open  
    from_database=from_database, ignore_cache=ignore_cache, **kw))  
  File "C:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\core\commands\open.py", line 81, in open  
    filename, format=format, name=name, ignore_cache=ignore_cache, **kw)  
  File "C:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\core\commands\open.py", line 62, in handle_unknown_kw  
    return f(*args, **kw)  
  File "C:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\core\fetch.py", line 433, in fetch_from_database  
    models, status = df.fetch(session, id, format=format,
ignore_cache=ignore_cache, **kw)  
  File "C:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\core\fetch.py", line 496, in fetch  
    return fetch(session, database_id, ignore_cache=ignore_cache, **kw)  
  File "C:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 327, in fetch_cb  
    return fetch_shim(session, identifier, **kw)  
  File "C:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 325, in fetch_shim  
    return f(session, identifier, database_name=database_name,
format_name=format_name, **kw)  
  File "C:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\atomic\pdb\\__init__.py", line 31, in fetch_from_database  
    return fetcher(session, identifier, ignore_cache=ignore_cache, **kw)  
  File "C:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\atomic\pdb\pdb.py", line 133, in fetch_pdb  
    models, status = io.open_data(session, filename, format='pdb',
name=pdb_id, **kw)  
  File "C:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\core\io.py", line 404, in open_data  
    models, status = open_func(*args, **kw)  
  File "C:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\atomic\pdb\\__init__.py", line 40, in open_file  
    coordsets=coordsets, atomic=atomic, max_models=max_models,
log_info=log_info)  
  File "C:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\atomic\pdb\pdb.py", line 35, in open_pdb  
    for p in pointers]  
  File "C:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\atomic\pdb\pdb.py", line 35, in <listcomp>  
    for p in pointers]  
  File "C:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\atomic\structure.py", line 2157, in __init__  
    self._set_chain_descriptions(self.session)  
  File "C:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\atomic\structure.py", line 2385, in _set_chain_descriptions  
    chains = sorted(self.chains, key=lambda c: c.chain_id)  
  File "C:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\atomic\molc.py", line 161, in get_prop  
    vcount = getattr(self, value_count)  
  File "C:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\atomic\molc.py", line 93, in get_prop  
    cget(self._c_pointer_ref, 1, v_ref)  
IndexError: invalid map<K, T> key  
  

IndexError: invalid map key  
  
File "C:\cygwin64\home\gregc\src\chimerax\ChimeraX.app\bin\lib\site-
packages\chimerax\atomic\molc.py", line 93, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
  
See log for complete Python traceback.  
  
If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu and
describe what you were doing and include a copy of the contents of the log.
Don't include any data you wish to remain private since a publicly viewable
bug report will be created.  




OpenGL version: 3.3.0 NVIDIA 391.24
OpenGL renderer: GeForce GTX 970/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Eric Pettersen]

Seems to have "fixed itself" (reverse bitrot)