Model.delete() called twice?

[tic20@…]

The following bug report has been submitted:
Platform:        Linux-3.10.0-957.12.2.el7.x86_64-x86_64-with-centos-7.6.1810-Core
ChimeraX Version: 0.91 (2019-06-29)
Description
Got the below error after associating a cryo-EM map and model in Clipper, then closing the lot. First time I've seen it, and as you can see from the log I did the same for a few other models/maps without incident. Not sure what's going on here.

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.91 (2019-06-29)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 5k12

Summary of feedback from opening 5k12 fetched from pdb  
---  
note | Fetching compressed mmCIF 5k12 from
http://files.rcsb.org/download/5k12.cif  
  
5k12 title:  
Cryo-EM structure of glutamate dehydrogenase at 1.8 A resolution [more
info...]  
  
Chain information for 5k12 #1  
---  
Chain | Description  
A B C D E F | Glutamate dehydrogenase 1, mitochondrial  
  
  

> open 8194 fromDatabase emdb

Summary of feedback from opening 8194 fetched from emdb  
---  
note | Fetching compressed map 8194 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-8194/map/emd_8194.map.gz  
  
Opened emd_8194.map, grid size 234,234,234, pixel 0.637, shown at level 0.013,
step 1, values float32  

> clipper associate #2 toModel #1

5k12 title:  
Cryo-EM structure of glutamate dehydrogenase at 1.8 A resolution [more
info...]  
  
Chain information for 5k12  
---  
Chain | Description  
1.3/A 1.3/B 1.3/C 1.3/D 1.3/E 1.3/F | Glutamate dehydrogenase 1, mitochondrial  
  

> clashes #1

24 clashes  

> close #1

> open 5a1a

Summary of feedback from opening 5a1a fetched from pdb  
---  
notes | Fetching compressed mmCIF 5a1a from
http://files.rcsb.org/download/5a1a.cif  
Fetching CCD PTQ from http://ligand-expo.rcsb.org/reports/P/PTQ/PTQ.cif  
  
5a1a title:  
2.2 A resolution cryo-EM structure of beta-galactosidase in complex with a
cell-permeant inhibitor [more info...]  
  
Chain information for 5a1a #1  
---  
Chain | Description  
A B C D | β-galactosidase  
  
Non-standard residues in 5a1a #1  
---  
MG — magnesium ion  
NA — sodium ion  
PTQ — 2-phenylethyl 1-thio-beta-D-galactopyranoside (2-Phenylethyl beta-D-
thiogalactoside, PETG)  
  
  

> open 2984 fromDatabase emdb

Summary of feedback from opening 2984 fetched from emdb  
---  
note | Fetching compressed map 2984 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-2984/map/emd_2984.map.gz  
  
Opened emd_2984.map, grid size 292,292,292, pixel 0.637, shown at level
0.0469, step 2, values float32  

> clipper associate #2 toModel #1

5a1a title:  
2.2 A resolution cryo-EM structure of beta-galactosidase in complex with a
cell-permeant inhibitor [more info...]  
  
Chain information for 5a1a  
---  
Chain | Description  
1.3/A 1.3/B 1.3/C 1.3/D | β-galactosidase  
  
Non-standard residues in 5a1a #1.3  
---  
MG — magnesium ion  
NA — sodium ion  
PTQ — 2-phenylethyl 1-thio-beta-D-galactopyranoside (2-Phenylethyl beta-D-
thiogalactoside, PETG)  
  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> addh

Summary of feedback from adding hydrogens to 5a1a #1.3  
---  
notes | Termini for 5a1a (#1.3) chain A determined from SEQRES records  
Termini for 5a1a (#1.3) chain B determined from SEQRES records  
Termini for 5a1a (#1.3) chain C determined from SEQRES records  
Termini for 5a1a (#1.3) chain D determined from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 2, /B MET 2, /C MET
2, /D MET 2  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A LYS 1023, /B LYS 1023, /C
LYS 1023, /D LYS 1023  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue /A LYS 1023  
Missing OXT added to C-terminal residue /B LYS 1023  
Missing OXT added to C-terminal residue /C LYS 1023  
Missing OXT added to C-terminal residue /D LYS 1023  
5776 hydrogen bonds  
32880 hydrogens added  
  

> hide HC

> select up

40 atoms, 41 bonds, 1 model selected  
Bad residue number: 194  
Doing nothing  

> show selAtoms

> close #1

> open 6nwp

Summary of feedback from opening 6nwp fetched from pdb  
---  
note | Fetching compressed mmCIF 6nwp from
http://files.rcsb.org/download/6nwp.cif  
  
6nwp title:  
Chronic traumatic encephalopathy Type I τ filament [more info...]  
  
Chain information for 6nwp #1  
---  
Chain | Description  
A B C D E F | Microtubule-associated protein τ  
  
6nwp title:  
Chronic traumatic encephalopathy Type I τ filament [more info...]  
  
Chain information for 6nwp  
---  
Chain | Description  
1.3/A 1.3/B 1.3/C 1.3/D 1.3/E 1.3/F | Microtubule-associated protein τ  
  
  

> view #1

> cofr centerOfView

> open 0527 fromDatabase emdb

Summary of feedback from opening 0527 fetched from emdb  
---  
note | Fetching compressed map 0527 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-0527/map/emd_0527.map.gz  
  
Opened emd_0527.map, grid size 256,256,256, pixel 1.15, shown at level 0.021,
step 1, values float32  

> clipper associate #2 toModel #1

> close #1

Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/objects.py", line 73, in _model_deleted_cb  
del self._handlers[model]  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/weakref.py", line 146, in
__delitem__  
del self.data[key]  
KeyError: <chimerax.core.models.Surface object at 0x7f5f6a57a6d8>  
  
Error processing trigger "deleted": :  
KeyError:  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/weakref.py", line 146, in
__delitem__  
del self.data[key]  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 415.27
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Tom Goddard]

Tristan says he has fixed bug #2159 which Eric encountered while trying to debug this error.

[Tom Goddard]

I added code in Model.delete() to raise an error if a Model is deleted twice so it will be easier to debug this situation in the future.