Opened 6 years ago

Closed 6 years ago

Last modified 6 years ago

#2620 closed defect (fixed)

Sequence viewer using deleted residues

Reported by: Elaine Meng Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Sequence Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

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 <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.  
  

> 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 <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.  
  

> 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: <chimerax.atomic.molobject.Sequence object at 0x138a69b50>  
  
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: <chimerax.atomic.molobject.Sequence object at 0x140271a10>  
  
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: <chimerax.atomic.molobject.Sequence object at 0x14e93d110>  
  
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: <chimerax.atomic.molobject.Sequence object at 0x12aba77d0>  
  
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: <chimerax.atomic.molobject.Sequence object at 0x12f2ea810>  
  
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: <chimerax.atomic.molobject.Sequence object at 0x12f2ea350>  
  
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: <chimerax.atomic.molobject.Sequence object at 0x13518d090>  
  
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: <chimerax.atomic.molobject.Sequence object at 0x13239b510>  
  
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 <listcomp>  
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

model-pdl-fig.cxs​

Attachments (1)

model-pdl-fig.cxs​ (344.9 KB ) - added by Elaine Meng 6 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (5)

by Elaine Meng, 6 years ago

Attachment: model-pdl-fig.cxs​ added

Added by email2trac

in reply to:  2 comment:1 by Elaine Meng, 6 years ago 

Also (relatively minor) the additional scores that were in the Modeller Results panel are not restored with the session.  Those cells in the table of scores are just blank.

comment:2 by Eric Pettersen, 6 years ago

Component: Unassigned → Sequence
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Sequence viewer using deleted residues

comment:3 by Eric Pettersen, 6 years ago

Resolution: → fixed
Status: accepted → closed

Was fixed in October, but the fix only helps new sessions, since needed info wasn't saved into older sessions.

comment:4 by Eric Pettersen, 6 years ago

The "scores not saved" thing is also an old-session bug. It was fixed in June

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