Associating structures with sequence: local variable 'best_match_map' referenced before assignment

[Elaine Meng]

The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.8 (2018-08-22)
Description
open 1plx
in Log, click chain description "Met-enkephalin 1" to show sequence

Log:
UCSF ChimeraX version: 0.8 (2018-08-22)  
How to cite UCSF ChimeraX  

open 1plx

Summary of feedback from opening 1plx fetched from pdb  
---  
warning | Found disconnected atom H1 that is not in residue template for TYR
#1 in chain A  
  
1plx title:  
NMR structure of Methionine-Enkephalin in fast tumbling Bicelles/DMPG
[more&nbspinfo...;]  
  
Chain information for 1plx #1.80  
---  
Chain | Description  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A
1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A 1.21/A 1.22/A 1.23/A
1.24/A 1.25/A 1.26/A 1.27/A 1.28/A 1.29/A 1.30/A 1.31/A 1.32/A 1.33/A 1.34/A
1.35/A 1.36/A 1.37/A 1.38/A 1.39/A 1.40/A 1.41/A 1.42/A 1.43/A 1.44/A 1.45/A
1.46/A 1.47/A 1.48/A 1.49/A 1.50/A 1.51/A 1.52/A 1.53/A 1.54/A 1.55/A 1.56/A
1.57/A 1.58/A 1.59/A 1.60/A 1.61/A 1.62/A 1.63/A 1.64/A 1.65/A 1.66/A 1.67/A
1.68/A 1.69/A 1.70/A 1.71/A 1.72/A 1.73/A 1.74/A 1.75/A 1.76/A 1.77/A 1.78/A
1.79/A 1.80/A | Met-enkephalin 1  
  
  

sequence chain
#1.1/A#1.2/A#1.3/A#1.4/A#1.5/A#1.6/A#1.7/A#1.8/A#1.9/A#1.10/A#1.11/A#1.12/A#1.13/A#1.14/A#1.15/A#1.16/A#1.17/A#1.18/A#1.19/A#1.20/A#1.21/A#1.22/A#1.23/A#1.24/A#1.25/A#1.26/A#1.27/A#1.28/A#1.29/A#1.30/A#1.31/A#1.32/A#1.33/A#1.34/A#1.35/A#1.36/A#1.37/A#1.38/A#1.39/A#1.40/A#1.41/A#1.42/A#1.43/A#1.44/A#1.45/A#1.46/A#1.47/A#1.48/A#1.49/A#1.50/A#1.51/A#1.52/A#1.53/A#1.54/A#1.55/A#1.56/A#1.57/A#1.58/A#1.59/A#1.60/A#1.61/A#1.62/A#1.63/A#1.64/A#1.65/A#1.66/A#1.67/A#1.68/A#1.69/A#1.70/A#1.71/A#1.72/A#1.73/A#1.74/A#1.75/A#1.76/A#1.77/A#1.78/A#1.79/A#1.80/A

Alignment identifier is 1  
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/ui/gui.py", line 504, in customEvent  
    func(*args, **kw)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/widgets/htmlview.py", line 278, in defer  
    cxcmd(session, topic)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/widgets/htmlview.py", line 377, in cxcmd  
    ti.execute()  
  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 205, 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 2561, 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/seqalign/cmd.py", line 150, in seqalign_chain  
    alignment.associate(chain, keep_intrinsic=True)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/seqalign/alignment.py", line 245, in associate  
    if not best_match_map or errors < best_errors:  
UnboundLocalError: local variable 'best_match_map' referenced before
assignment  
  

UnboundLocalError: local variable 'best_match_map' referenced before
assignment  
  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/seqalign/alignment.py", line 245, in associate  
if not best_match_map or errors < best_errors:  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102
OpenGL renderer: NVIDIA GeForce GTX 675MX OpenGL Engine
OpenGL vendor: NVIDIA Corporation

[pett]

Fixed; one of the changes necessitated when translating the associate() code from Chimera 1 to ChimeraX wasn't quite right.