MatchMaker specific chain-chain pairing: wrapped C/C++ object of type ChainMenuButton has been deleted

[shon.a.koren@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
Tried aligning using MatchMaker two chains (6zr2/D and 6ztq/D). I have lots of structures open and I've moved some of them, which I don't think chimera likes much.

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\Users\shona\OneDrive\Desktop\6zr2.pdb format pdb

No such file/path: C:\Users\shona\OneDrive\Desktop\6zr2.pdb  

> open 6zr2 format mmcif fromDatabase pdb

6zr2 title:  
Cryo-EM structure of respiratory complex I in the active state from Mus
musculus at 3.1 A [more info...]  
  
Chain information for 6zr2 #1  
---  
Chain | Description  
A | NADH-ubiquinone oxidoreductase chain 3  
B | NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial  
C | NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial  
D | NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial  
E | NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial  
F | NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial  
G | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial  
H | NADH-ubiquinone oxidoreductase chain 1  
I | NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial  
J | NADH-ubiquinone oxidoreductase chain 6  
K | NADH-ubiquinone oxidoreductase chain 4L  
L | NADH-ubiquinone oxidoreductase chain 5  
M | NADH-ubiquinone oxidoreductase chain 4  
N | NADH-ubiquinone oxidoreductase chain 2  
O | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 10, mitochondrial  
P | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 9, mitochondrial  
Q | NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial  
R | NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial  
S | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 2  
T U | Acyl carrier protein, mitochondrial  
V | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 5  
W | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 6  
X | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 8  
Y | MCG5603  
Z | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 13  
a | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 1  
b | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 3  
c | NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial  
d | NADH dehydrogenase [ubiquinone] 1 subunit C2  
e | NADH dehydrogenase [ubiquinone] iron-sulfur protein 5  
f | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 1  
g | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 11, mitochondrial  
h | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 5, mitochondrial  
i | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 6  
j | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 2, mitochondrial  
k | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 3  
l | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 8, mitochondrial  
m | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 4  
n | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 9  
o | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 7  
p | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 10  
q | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 12  
r | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 7  
s | NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial  
  
Non-standard residues in 6zr2 #1  
---  
3PE — 1,2-diacyl-Sn-glycero-3-phosphoethanolamine (3-Sn-
phosphatidylethanolamine)  
ATP — adenosine-5'-triphosphate  
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)  
EHZ — ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-
butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate  
FES — FE2/S2 (inorganic) cluster  
FMN — flavin mononucleotide (riboflavin monophosphate)  
NDP — nadph dihydro-nicotinamide-adenine-dinucleotide phosphate  
PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine)  
SF4 — iron/sulfur cluster  
ZN — zinc ion  
  

> select all

67042 atoms, 68744 bonds, 38 pseudobonds, 8216 residues, 3 models selected  

> hide sel atoms

> set bgColor white

> show sel cartoons

> color sel lightgrey

> set bgColor black

> color /D red

> color /D:314 pink

> color /D:314 green

> select clear

> select all

67042 atoms, 68744 bonds, 38 pseudobonds, 8216 residues, 3 models selected  

> hide sel cartoons

> select /D

3464 atoms, 3554 bonds, 430 residues, 1 model selected  

> show sel cartoons

> select clear

> select /D:314

6 atoms, 5 bonds, 1 residue, 1 model selected  

> style sel ball

Changed 6 atom styles  

> show sel target ab

> select clear

> ui tool show "Show Sequence Viewer"

> sequence chain /D

Alignment identifier is 1/D  

> select /D:132

7 atoms, 7 bonds, 1 residue, 1 model selected  

> color sel lime

> show sel target ab

> style sel ball

Changed 6 atom styles  

> color sel lime

> show sel target ab

> style sel ball

Changed 6 atom styles  

> color /D tan

> color /D:314 298 113 lightgreen

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color /D:314 :298 :113 lightgreen

> color /D:314 :293 :113 lightgreen

> color /D:298 tan

> select clear

> select /D:293@CA

1 atom, 1 residue, 1 model selected  

> color sel lime

> select up

18 atoms, 15 bonds, 3 residues, 1 model selected  

> color sel lime

> select clear

> select ::name="SF4"

48 atoms, 72 bonds, 6 residues, 1 model selected  

> show sel target ab

> surface sel

> color (#!1 & sel) byhetero

> select clear

> select up

40 atoms, 60 bonds, 5 residues, 4 models selected  

> surface hidePatches (#!1 & sel)

> hide (#!1 & sel) target a

> select up

58 atoms, 75 bonds, 8 residues, 4 models selected  

> surface (#!1 & sel)

> hide (#!1 & sel) target a

> surface (#!1 & sel)

> color (#!1 & sel) lime

> select clear

> select /D:293

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /D:113

6 atoms, 5 bonds, 1 residue, 1 model selected  

> surface (#!1 & sel)

> surface hidePatches (#!1 & sel)

> surface (#!1 & sel)

> select clear

> select /D:113

6 atoms, 5 bonds, 1 residue, 1 model selected  

> show (#!1 & sel) target ab

> surface hidePatches (#!1 & sel)

> style (#!1 & sel) sphere

Changed 6 atom styles  

> select /D:314

6 atoms, 5 bonds, 1 residue, 1 model selected  

> show (#!1 & sel) target ab

> style (#!1 & sel) sphere

Changed 12 atom styles  

> select clear

> set bgColor white

> select /D:293@CB

1 atom, 1 residue, 1 model selected  

> select up

6 atoms, 5 bonds, 1 residue, 1 model selected  

> set bgColor black

> ui tool show H-Bonds

> select up

12 atoms, 10 bonds, 2 residues, 2 models selected  

> select up

18 atoms, 15 bonds, 3 residues, 2 models selected  

> hbonds sel color #ffffff

8 hydrogen bonds found  

> color /D:299-315 pink

> color /D:299-315 red

> color /D:314 lime

> select clear

> select clear

> select clear

> select clear

> select #1.8

8 pseudobonds, 1 model selected  
No visible atoms, bonds, or surfaces selected  

> color sel blue

> select clear

> set bgColor white

> select /D:140

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /D:139

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select clear

> select /D:314@SG

1 atom, 1 residue, 1 model selected  

> select up

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select up

12 atoms, 10 bonds, 2 residues, 2 models selected  

> select up

18 atoms, 15 bonds, 3 residues, 2 models selected  

> ui tool show Contacts

> contacts sel overlapCutoff -15.0 interModel false select true
> makePseudobonds false

19329 contacts  

> contacts sel overlapCutoff -15.0 resSeparation 5 interModel false select
> true makePseudobonds false

1976983 contacts  

> contacts sel overlapCutoff -4.0 resSeparation 5 interModel false select true
> makePseudobonds false

216710 contacts  

> contacts sel resSeparation 5 interModel false select true makePseudobonds
> false

7128 contacts  

> select /D:314 :293 :113

18 atoms, 15 bonds, 3 residues, 1 model selected  

> contacts sel resSeparation 5 interModel false select true makePseudobonds
> false

19 contacts  

> select /D:314 :293 :113

18 atoms, 15 bonds, 3 residues, 1 model selected  
Illegal contacts 'color' attribute value (Color([1.0, 0.6666667, 0.0, 1.0])),
leaving attribute unchanged  
Illegal contacts 'color' attribute value (Color([1.0, 1.0, 1.0, 1.0])),
leaving attribute unchanged  
Illegal contacts 'color' attribute value (Color([1.0, 1.0, 1.0, 1.0])),
leaving attribute unchanged  
Illegal contacts 'color' attribute value (Color([1.0, 1.0, 1.0, 1.0])),
leaving attribute unchanged  

> select clear

> select /D:293@CA

1 atom, 1 residue, 1 model selected  

> select /D:314 :293 :113

18 atoms, 15 bonds, 3 residues, 1 model selected  

> ui tool show Contacts

> contacts sel resSeparation 5 interModel false select true makePseudobonds
> false

19 contacts  

> select /D:314 :293 :113

18 atoms, 15 bonds, 3 residues, 1 model selected  

> contacts sel resSeparation 5 interModel false select true

19 contacts  

> select clear

> set bgColor black

> set bgColor white

> color (#!1 & sel) red

> select clear

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> lighting soft

> lighting full

> lighting simple

> lighting soft

> ui mousemode right clip

> select /D:160 :59 purple

Expected a keyword  

> color /D:160 :59 purple

> color /D:108 :190 :85 :105 cyan

> select /D:108 190 85 105 160 59

Expected a keyword  

> select /D:108 :190 :85 :105 :160 :59

64 atoms, 61 bonds, 6 residues, 1 model selected  

> show (#!1 & sel) target ab

> style (#!1 & sel) ball

Changed 64 atom styles  

> select clear

> set bgColor black

> set bgColor white

> select up

29 atoms, 28 bonds, 4 residues, 2 models selected  

> select up

3464 atoms, 3554 bonds, 430 residues, 2 models selected  

> select clear

> graphics silhouettes false

> graphics silhouettes true

> open 6Q9E

Summary of feedback from opening 6Q9E fetched from pdb  
---  
warning | Unable to fetch template for 'U10': might have incorrect bonds  
note | Fetching compressed mmCIF 6q9e from
http://files.rcsb.org/download/6q9e.cif  
  
6q9e title:  
Complex III2 focused refinement from Ovine respiratory supercomplex I+III2
[more info...]  
  
Chain information for 6q9e #2  
---  
Chain | Description  
a1 a3 | Ubiquinol-cytochrome c reductase core protein 1  
a2 a4 | Ubiquinol-cytochrome c reductase core protein 2  
b1 b2 | Cytochrome b  
c1 c2 | Cytochrome c1  
d1 d2 | Cytochrome b-c1 complex subunit 7  
f1 f2 | Cytochrome b-c1 complex subunit Rieske, mitochondrial  
h1 h2 | Cytochrome b-c1 complex subunit 6  
i1 i2 | Ubiquinol-cytochrome c reductase, complex III subunit X  
q1 q2 | Ubiquinol-cytochrome c reductase complex III subunit VII  
x1 x2 | Cytochrome b-c1 complex subunit Rieske, mitochondrial  
  
Non-standard residues in 6q9e #2  
---  
3PE — 1,2-diacyl-Sn-glycero-3-phosphoethanolamine (3-Sn-
phosphatidylethanolamine)  
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)  
FES — FE2/S2 (inorganic) cluster  
HEC — heme C  
HEM — protoporphyrin IX containing Fe (HEME)  
U10 — ubiquinone-10 (Coenzyme Q10)  
  

> select #2/h2:29@NZ

1 atom, 1 residue, 1 model selected  

> select up

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

154 atoms, 153 bonds, 19 residues, 1 model selected  

> select up

532 atoms, 540 bonds, 65 residues, 1 model selected  

> select up

31997 atoms, 32773 bonds, 4008 residues, 1 model selected  

> hide sel atoms

> select ::name="U10"

76 atoms, 76 bonds, 3 residues, 1 model selected  

> show sel atoms

> ui tool show Contacts

> contacts sel resSeparation 5 interModel false reveal true

100 contacts  

> contacts sel overlapCutoff 1.0 resSeparation 5 interModel false reveal true

No contacts  

> contacts sel overlapCutoff -10.0 interModel false reveal true

30021 contacts  

> contacts sel overlapCutoff -10.0 interModel false select true reveal true

30021 contacts  

> hide sel atoms

> show sel cartoons

> hide sel atoms

> select #2/U10

Nothing selected  

> select #2:U10

76 atoms, 76 bonds, 3 residues, 1 model selected  

> show sel atoms

> hide #2.3 models

> select #2

31997 atoms, 32773 bonds, 30068 pseudobonds, 4008 residues, 4 models selected  

> ui mousemode right "translate selected models"

> show cartoons #2

Expected ',' or a keyword  

> show #2 cartoons

> select clear

> open

Missing or invalid "fileNames" argument: Expected a file name  

> open C:\Users\shona\OneDrive\Desktop/U10.cif

> open C:\Users\shona\OneDrive\Desktop/U10.cif name U10

> open C:/Users/shona/OneDrive/Desktop/U10.cif

> hide #2 cartoons

> hide #2 surfaces

> hide #2 atoms

> show #2:U10

> select #2/b1:406@C1

1 atom, 1 residue, 1 model selected  

> select up

28 atoms, 28 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected atoms"

> surface sel

> surface style #2 mesh

> select #1/D:412

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select up

84 atoms, 83 bonds, 12 residues, 2 models selected  

> select up

3464 atoms, 3554 bonds, 430 residues, 2 models selected  

> select up

67042 atoms, 68744 bonds, 8216 residues, 2 models selected  

> ui mousemode right "translate selected models"

> select #2/b1:406@C1M

1 atom, 1 residue, 1 model selected  

> select up

28 atoms, 28 bonds, 1 residue, 2 models selected  

> ui mousemode right "rotate selected models"

> ui mousemode right clip

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right "translate selected atoms"

> open 6ztq

Summary of feedback from opening 6ztq fetched from pdb  
---  
warning | Unable to fetch template for 'HQH': might have incorrect bonds  
note | Fetching compressed mmCIF 6ztq from
http://files.rcsb.org/download/6ztq.cif  
  
6ztq title:  
Cryo-EM structure of respiratory complex I from Mus musculus inhibited by
piericidin A at 3.0 A [more info...]  
  
Chain information for 6ztq #3  
---  
Chain | Description  
A | NADH-ubiquinone oxidoreductase chain 3  
B | NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial  
C | NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial  
D | NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial  
E | NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial  
F | NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial  
G | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial  
H | NADH-ubiquinone oxidoreductase chain 1  
I | NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial  
J | NADH-ubiquinone oxidoreductase chain 6  
K | NADH-ubiquinone oxidoreductase chain 4L  
L | NADH-ubiquinone oxidoreductase chain 5  
M | NADH-ubiquinone oxidoreductase chain 4  
N | NADH-ubiquinone oxidoreductase chain 2  
O | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 10, mitochondrial  
P | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 9, mitochondrial  
Q | NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial  
R | NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial  
S | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 2  
T U | Acyl carrier protein, mitochondrial  
V | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 5  
W | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 6  
X | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 8  
Y | MCG5603  
Z | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 13  
a | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 1  
b | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 3  
c | NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial  
d | NADH dehydrogenase [ubiquinone] 1 subunit C2  
e | NADH dehydrogenase [ubiquinone] iron-sulfur protein 5  
f | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 1  
g | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 11, mitochondrial  
h | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 5, mitochondrial  
i | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 6  
j | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 2, mitochondrial  
k | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 3  
l | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 8, mitochondrial  
m | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 4  
n | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 9  
o | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 7  
p | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 10  
q | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 12  
r | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 7  
s | NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial  
  
Non-standard residues in 6ztq #3  
---  
3PE — 1,2-diacyl-Sn-glycero-3-phosphoethanolamine (3-Sn-
phosphatidylethanolamine)  
ATP — adenosine-5'-triphosphate  
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)  
EHZ — ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-
butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate  
FES — FE2/S2 (inorganic) cluster  
FMN — flavin mononucleotide (riboflavin monophosphate)  
HQH — Piericidin A  
NDP — nadph dihydro-nicotinamide-adenine-dinucleotide phosphate  
PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine)  
SF4 — iron/sulfur cluster  
ZN — zinc ion  
  

> select #3

67072 atoms, 68773 bonds, 38 pseudobonds, 8217 residues, 3 models selected  

> ui mousemode right "translate selected models"

> hide sel atoms

> show sel cartoons

> select clear

> color #3 lightgrey

> color #3/D red

> hide #3 cartoons

> show #3:D cartoons

> show #3:D cartoons

> select #3/D

3545 atoms, 3634 bonds, 432 residues, 1 model selected  

> cartoon sel

> color sel tan

> show #3:HGH atoms

> show #3:HGH

> select ::name="HQH"

30 atoms, 30 bonds, 1 residue, 1 model selected  

> show sel target ab

> select ::name="SF4"

96 atoms, 144 bonds, 12 residues, 2 models selected  

> select #3:SF4

48 atoms, 72 bonds, 6 residues, 1 model selected  

> show sel surfaces

> ui tool show Matchmaker

> matchmaker #1/D to #3/D pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6ztq, chain D (#3) with 6zr2, chain D (#1), sequence alignment
score = 2333.1  
RMSD between 429 pruned atom pairs is 0.238 angstroms; (across all 430 pairs:
0.267)  
  
Traceback (most recent call last):  
File "D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\triggerset.py", line
130, in invoke  
return self._func(self._name, data)  
File "D:\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File "D:\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> hide #!3 models

> hide #!2 models

> show #!3 models

> hide #3

Traceback (most recent call last):  
File "D:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\triggerset.py", line
130, in invoke  
return self._func(self._name, data)  
File "D:\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted  
  
File "D:\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> save "C:/Users/shona/OneDrive/Desktop/bugged session.cxs"




OpenGL version: 3.3.0 NVIDIA 445.87
OpenGL renderer: GeForce GTX 1050/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Inspiron 5577
OS: Microsoft Windows 10 Pro (Build 19041)
Memory: 17,035,116,544
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    gdcm: 2.8.8
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5+mkl
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pywin32: 228
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2
    WMI: 1.5.1
File attachment: bugged session.cxs

bugged session.cxs​

[shon.a.koren@…]

Added by email2trac

[Eric Pettersen]

Hi Shon,

Thanks for reporting this problem. This bug is fixed in the current daily build, so if you use that then you should no longer encounter this problem. Sorry for the hassle.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab