deleting scraggly parts of models from Modeller gives Error processing trigger "modified"

[Elaine Meng]

open 3bp5
open uniprot:pdcd1_human
sequence associate /A pdcd1_human
toolshed show "Modeller Comparative"
modeller comparative pdcd1_human:1 multichain true numModels 3 fast false hetPreserve false hydrogens false waterPreserve false
[... select untemplated part by clicking inside gray box in Sequence]
del sel

Traceback (most recent call last):

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/triggerset.py", line 130, in invoke

return self._func(self._name, data)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/seqalign/alignment.py", line 520, in _mmap_mod_cb

self._notify_observers("modify association", ("modify association", [match_map]))

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/seqalign/alignment.py", line 531, in _notify_observers

recipient.alignment_notification(note_name, note_data)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/seq-view/tool.py", line 450, in alignment_notification

self.seq_canvas.assoc_mod(aseq)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/seq-view/seq_canvas.py", line 417, in assoc_mod

self.lead_block.assoc_mod(aseq)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/seq-view/seq_canvas.py", line 1703, in assoc_mod

self._assoc_res_bind(item, aseq, self.seq_offset+i)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/seq-view/seq_canvas.py", line 1679, in _assoc_res_bind

item.setToolTip(self._mouse_res_text(aseq, index))

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/seq-view/seq_canvas.py", line 2371, in _mouse_res_text

res_text = "\n".join([str(r) for r in residues])

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/seq-view/seq_canvas.py", line 2371, in <listcomp>

res_text = "\n".join([str(r) for r in residues])

File "cymol.pyx", line 876, in chimerax.atomic.cymol.CyResidue.str
File "cymol.pyx", line 1484, in chimerax.atomic.cymol.CyResidue.string
File "cymol.pyx", line 1040, in chimerax.atomic.cymol.CyResidue.insertion_code.get

RuntimeError: Residue already deleted

Error processing trigger "modified":
RuntimeError: Residue already deleted

File "cymol.pyx", line 1040, in chimerax.atomic.cymol.CyResidue.insertion_code.get

See log for complete Python traceback.

Traceback (most recent call last):

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/triggerset.py", line 130, in invoke

return self._func(self._name, data)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/seqalign/alignment.py", line 520, in _mmap_mod_cb

self._notify_observers("modify association", ("modify association", [match_map]))

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/seqalign/alignment.py", line 531, in _notify_observers

recipient.alignment_notification(note_name, note_data)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/seq-view/tool.py", line 450, in alignment_notification

self.seq_canvas.assoc_mod(aseq)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/seq-view/seq_canvas.py", line 417, in assoc_mod

self.lead_block.assoc_mod(aseq)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/seq-view/seq_canvas.py", line 1703, in assoc_mod

self._assoc_res_bind(item, aseq, self.seq_offset+i)

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/seq-view/seq_canvas.py", line 1679, in _assoc_res_bind

item.setToolTip(self._mouse_res_text(aseq, index))

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/seq-view/seq_canvas.py", line 2371, in _mouse_res_text

res_text = "\n".join([str(r) for r in residues])

File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/seq-view/seq_canvas.py", line 2371, in <listcomp>

res_text = "\n".join([str(r) for r in residues])

File "cymol.pyx", line 876, in chimerax.atomic.cymol.CyResidue.str
File "cymol.pyx", line 1484, in chimerax.atomic.cymol.CyResidue.string
File "cymol.pyx", line 1040, in chimerax.atomic.cymol.CyResidue.insertion_code.get

RuntimeError: Residue already deleted

Error processing trigger "modified":
RuntimeError: Residue already deleted

File "cymol.pyx", line 1040, in chimerax.atomic.cymol.CyResidue.insertion_code.get

See log for complete Python traceback.

[Eric Pettersen]

The association info was being updated on a piecemeal basis, so it wasn't all consistent when used. Needed to wait for the "atomic changes" trigger to completely finish before updating association info.