id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2620 Sequence viewer using deleted residues Elaine Meng Eric Pettersen "{{{ The following bug report has been submitted: Platform: Darwin-17.7.0-x86_64-i386-64bit ChimeraX Version: 0.91 (2019-11-27) Description open attached session and enter command ""close"" Log: > open /Users/meng/Desktop/startup.cxc > alias reset view orient; view initial > alias start toolshed show $1 > alias whereprefs info path user unversioned config executed startup.cxc UCSF ChimeraX version: 0.91 (2019-11-27) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open model*cxc > open 3bp5 3bp5 title: Crystal structure of the mouse PD-1 and PD-L2 complex [more info...] Chain information for 3bp5 #1 --- Chain | Description A | Programmed cell death protein 1 B | Programmed cell death 1 ligand 2 Non-standard residues in 3bp5 #1 --- GOL — glycerol (glycerin; propane-1,2,3-triol) > open uniprot:pdcd1_human Summary of feedback from opening pdcd1_human fetched from uniprot --- note | Alignment identifier is pdcd1_human Opened UniProt pdcd1_human > sequence associate /A pdcd1_human Associated 3bp5 chain A to pdcd1_human with 41 mismatches and/or gaps > open uniprot:q2lc89_human Summary of feedback from opening q2lc89_human fetched from uniprot --- note | Alignment identifier is q2lc89_human Opened UniProt q2lc89_human > sequence associate /B q2lc89_human:1 Associated 3bp5 chain B to q2lc89_human with 57 mismatches and/or gaps executed model-pdl-setup.cxc > toolshed show ""Modeller Comparative"" > modeller comparative pdcd1_human:1,q2lc89_human:1 multichain true numModels > 3 fast false hetPreserve false hydrogens false waterPreserve false Web Service: Modeller9v8 is a Python wrapper that calls Modeller (v9.18) for protein structure modeling Opal service URL: http://webservices.rbvi.ucsf.edu/opal2/services/Modeller9v8Service Opal job id: appModeller9v8Service1574881587031-116540928 Opal status URL prefix: http://webservices.rbvi.ucsf.edu/appModeller9v8Service1574881587031-116540928 stdout.txt = standard output stderr.txt = standard error Modeller job ID appModeller9v8Service1574881587031-116540928 finished Matchmaker 3bp5, chain A (#1) with target, chain A (#), sequence alignment score = 418.4 Matchmaker 3bp5, chain B (#1) with target, chain B (#), sequence alignment score = 775.6 RMSD between 271 pruned atom pairs is 0.851 angstroms; (across all 305 pairs: 1.361) Matchmaker 3bp5, chain A (#1) with target, chain A (#), sequence alignment score = 418.4 Matchmaker 3bp5, chain B (#1) with target, chain B (#), sequence alignment score = 775.6 RMSD between 305 pruned atom pairs is 0.489 angstroms; (across all 305 pairs: 0.489) Matchmaker 3bp5, chain A (#1) with target, chain A (#), sequence alignment score = 418.4 Matchmaker 3bp5, chain B (#1) with target, chain B (#), sequence alignment score = 775.6 RMSD between 305 pruned atom pairs is 0.459 angstroms; (across all 305 pairs: 0.459) Associated target chain A to pdcd1_human with 0 mismatches Associated target chain A to pdcd1_human with 0 mismatches Associated target chain A to pdcd1_human with 0 mismatches Associated target chain B to q2lc89_human with 0 mismatches Associated target chain B to q2lc89_human with 0 mismatches Associated target chain B to q2lc89_human with 0 mismatches Chain information for target --- Chain | Description 2.1/A 2.2/A 2.3/A | No description available 2.1/B 2.2/B 2.3/B | No description available > modeller scores #2 refresh false > delete atoms 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 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 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. > delete bonds sel > delete 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 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 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. > modeller scores #2 refresh true > hide > show sel > label sel > label height 2 > label height 1 > hbonds #2.2 1016 hydrogen bonds found > select :pro 532 atoms, 541 bonds, 4 models selected > select :pro & ::label 532 atoms, 541 bonds, 4 models selected > label delete > color #1/a red > color #1/b orange > ~hbonds > hbonds /a restrict /b interModel false reveal true 75 hydrogen bonds found > hide > hbonds /a restrict /b interModel false reveal true 75 hydrogen bonds found > select clear > cartoon suppressBackboneDisplay false > delete solvent > label #2:pro > delete ~protein > hbonds /a restrict /b interModel false reveal true 52 hydrogen bonds found > select clear > close > close session > open model-pdl-fig.cxs Summary of feedback from opening model-pdl-fig.cxs --- warnings | Unable to restore ""SchemesManager"" object restore_snapshot for ""Labels"" returned None opened ChimeraX session > close 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 517, in _mmap_mod_cb self.disassociate(self._sseq_to_chain[match_map.struct_seq], demotion=True) KeyError: Error processing trigger ""modified"": KeyError: 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 517, in _mmap_mod_cb self.disassociate(self._sseq_to_chain[match_map.struct_seq], demotion=True) 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 517, in _mmap_mod_cb self.disassociate(self._sseq_to_chain[match_map.struct_seq], demotion=True) KeyError: Error processing trigger ""modified"": KeyError: 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 517, in _mmap_mod_cb self.disassociate(self._sseq_to_chain[match_map.struct_seq], demotion=True) 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 517, in _mmap_mod_cb self.disassociate(self._sseq_to_chain[match_map.struct_seq], demotion=True) KeyError: Error processing trigger ""modified"": KeyError: 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 517, in _mmap_mod_cb self.disassociate(self._sseq_to_chain[match_map.struct_seq], demotion=True) 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 517, in _mmap_mod_cb self.disassociate(self._sseq_to_chain[match_map.struct_seq], demotion=True) KeyError: Error processing trigger ""modified"": KeyError: 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 517, in _mmap_mod_cb self.disassociate(self._sseq_to_chain[match_map.struct_seq], demotion=True) 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 517, in _mmap_mod_cb self.disassociate(self._sseq_to_chain[match_map.struct_seq], demotion=True) KeyError: Error processing trigger ""modified"": KeyError: 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 517, in _mmap_mod_cb self.disassociate(self._sseq_to_chain[match_map.struct_seq], demotion=True) 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 517, in _mmap_mod_cb self.disassociate(self._sseq_to_chain[match_map.struct_seq], demotion=True) KeyError: Error processing trigger ""modified"": KeyError: 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 517, in _mmap_mod_cb self.disassociate(self._sseq_to_chain[match_map.struct_seq], demotion=True) 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 517, in _mmap_mod_cb self.disassociate(self._sseq_to_chain[match_map.struct_seq], demotion=True) KeyError: Error processing trigger ""modified"": KeyError: 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 517, in _mmap_mod_cb self.disassociate(self._sseq_to_chain[match_map.struct_seq], demotion=True) 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 517, in _mmap_mod_cb self.disassociate(self._sseq_to_chain[match_map.struct_seq], demotion=True) KeyError: Error processing trigger ""modified"": KeyError: 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 517, in _mmap_mod_cb self.disassociate(self._sseq_to_chain[match_map.struct_seq], demotion=True) 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/seq-view/seq_canvas.py"", line 229, in _actually_resize self._reformat() 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 1024, in _reformat self.label_width, self.font_pixels, self.numbering_widths, self.letter_gaps()) 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 1601, in __init__ self.layout_lines(alignment.seqs, self.normal_label_color) 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 2243, in layout_lines self._layout_line(line, label_color, bli, end) 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 2193, in _layout_line font=self._label_font(line)) 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 2133, in _label_font if self.has_associated_structures(line): 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 2071, in has_associated_structures and [chain for chain in line.match_maps.keys() if not chain.structure.deleted]: 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 2071, in and [chain for chain in line.match_maps.keys() if not chain.structure.deleted]: File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/attr_registration.py"", line 39, in _getattr_ return look_in_class._attr_registration.get_attr(attr_name) File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/attr_registration.py"", line 67, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None AttributeError: 'Sequence' object has no attribute 'structure' AttributeError: 'Sequence' object has no attribute 'structure' File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/attr_registration.py"", line 67, in get_attr raise AttributeError(""'%s' object has no attribute '%s'"" % (self.class_.__name__, attr_name)) from None 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 File attachment: model-pdl-fig.cxs }}} [attachment:""model-pdl-fig.cxs""] " defect closed normal Sequence fixed all ChimeraX