mmaker error: KeyError: ('<', 'M')

[Tom Goddard]

open 3iko
del ~/C
open ScNup84_7-488_506-726_new.pdb
mmaker #1 to #2:7-436

produces traceback

Traceback (most recent call last):
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/cmd_line/gui.py", line 146, in execute
cmd.run(cmd_text)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/cli.py", line 2221, in run
_used_aliases=used_aliases))
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/cli.py", line 2597, in call
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/cli.py", line 2206, in run
results.append(ci.function(session, kw_args))
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/match_maker/match.py", line 596, in cmd_match
gap_open_other=ogap, compute_ss=compute_ss, verbose=verbose)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/match_maker/match.py", line 296, in match
matrix, alg, gap_open, gap_extend, dssp_cache, align_kw)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/match_maker/match.py", line 56, in align
gap_open_other=-gap_open_other)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/seqalign/align_algs/NeedlemanWunsch/init.py", line 115, in nw
best = m[i1][i2] + evaluate(i1, i2)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/seqalign/align_algs/NeedlemanWunsch/init.py", line 81, in <lambda>
evaluate = lambda i1, i2: ss_fraction * ss_eval(i1, i2) + sim_fraction * prev_eval(i1, i2)
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/seqalign/align_algs/NeedlemanWunsch/init.py", line 46, in <lambda>
evaluate = lambda i1, i2: similarity_matrix[(s1[i1], s2[i2])]
KeyError: ('<', 'M')

[Eric Pettersen]

The domain-restricted sequence that was constructed wasn't having its characters correctly set