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#6885 closed defect (duplicate)

MatchMaker: wrapped C/C++ object of type ChainMenuButton has been deleted

Reported by:	disha-gajanan.hiregange@…	Owned by:	pett
Priority:	normal	Milestone:
Component:	Structure Comparison	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Linux-5.4.115-1.el8.elrepo.x86_64-x86_64-with-glibc2.14
ChimeraX Version: 1.2 (2021-04-27 05:33:30 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2 (2021-04-27)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open
> /yonath_group/disha/Gingivalis/delta266/models/comparision/SSU/rps3_chaiN_C.cxs
> format session

Log from Tue May 17 14:49:39 2022UCSF ChimeraX version: 1.2 (2021-04-27)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /yonath_group/sarit/pg_W83/RealSpaceRefine_26/50S_new_map_combined_WITH_MOD_2_3_real_space_refined_real_space_refined_026.pdb
> format pdb

Chain information for
50S_new_map_combined_WITH_MOD_2_3_real_space_refined_real_space_refined_026.pdb
#1  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
8 | No description available  
A | No description available  
B | No description available  
D | No description available  
E | No description available  
F | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
h | No description available  
  

> set bgColor white

> open /yonath_group/disha/Gingivalis/multimaps_new/50S_map.mrc

Opened 50S_map.mrc as #2, grid size 460,460,460, pixel 0.86, shown at level
0.00952, step 2, values float32  

> select #1

75706 atoms, 81315 bonds, 80 pseudobonds, 6308 residues, 2 models selected  

> show sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 53096 atom styles  

> style sel stick

Changed 75706 atom styles  

> volume style mesh

> volume #2 step 1

> volume #2 level 0.02

> select #1/A: 556-570

260 atoms, 290 bonds, 2 pseudobonds, 12 residues, 2 models selected  

> select

75706 atoms, 81315 bonds, 80 pseudobonds, 6308 residues, 4 models selected  

> select #1/A: 556-570

260 atoms, 290 bonds, 2 pseudobonds, 12 residues, 2 models selected  

> select ~sel

75446 atoms, 81025 bonds, 78 pseudobonds, 6296 residues, 4 models selected  

> hide sel atoms

> ui tool show "Surface Zone"

> surface zone #2 nearAtoms sel distance 5.12

> surface zone #2 nearAtoms sel distance 5.12

> surface zone #2 nearAtoms sel distance 5.12

> select clear

> select #1/A: 556-570

260 atoms, 290 bonds, 2 pseudobonds, 12 residues, 2 models selected  

> surface zone #2 nearAtoms sel distance 5.12

> surface zone #2 nearAtoms sel distance 5.12

> surface zone #2 nearAtoms sel distance 3.6

> volume step 1

> volume step 1

> volume step 2

> volume step 1

> volume step 1 subdivideSurface true

> volume step 1 subdivideSurface true

> \

Unknown command: \  

> \

Unknown command: \  

> select #1/A: 556-570

260 atoms, 290 bonds, 2 pseudobonds, 12 residues, 2 models selected  

> surface zone #2 nearAtoms sel distance 3.6

> surface zone #2 nearAtoms sel distance 3.6

> select #1/A: 556-570

260 atoms, 290 bonds, 2 pseudobonds, 12 residues, 2 models selected  

> select ~sel

75446 atoms, 81025 bonds, 78 pseudobonds, 6296 residues, 4 models selected  

> show sel atoms

> hide sel atoms

No atoms selected for zoning  

> volume step 1 subdivideSurface true

> select #1/A: 556-570

260 atoms, 290 bonds, 2 pseudobonds, 12 residues, 2 models selected  

> color sel byhetero

> ui tool show "Color Actions"

> ui tool show "Color Actions"

> color #1/A: 556-570 royal blue

> color sel byhetero

> color sel bypolymer

> select clear

> graphics silhouettes true

> graphics silhouettes false

> hide #!2 models

> graphics silhouettes true

> show #!2 models

> volume step 1 subdivideSurface false

> close session

> open
> /yonath_group/disha/Gingivalis/delta266/models/final_models/merged_FR_30S_D266_real_space_refined-
> coot-4.pdb

Chain information for merged_FR_30S_D266_real_space_refined-coot-4.pdb #1  
---  
Chain | Description  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
T | No description available  
a | No description available  
o | No description available  
  

> show cartoons

> hide atoms

> graphics silhouettes false

> open
> /yonath_group/disha/Gingivalis/delta266/models/comparision/7k00_aligned_d266_30s.pdb

Chain information for 7k00_aligned_d266_30s.pdb #2  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> select #2

149338 atoms, 154090 bonds, 1515 pseudobonds, 17719 residues, 3 models
selected  

> hide sel atoms

> show sel cartoons

> sequence chain #2/Z

Alignment identifier is 2/Z  

> sequence chain #2/0

Alignment identifier is 2/0  

> close session

> open
> /yonath_group/disha/Gingivalis/delta266/models/comparision/RNA/23s_merged_FR_30S_D266_real_space_refined-
> coot-5.pdb

Chain information for 23s_merged_FR_30S_D266_real_space_refined-coot-5.pdb #1  
---  
Chain | Description  
a | No description available  
  

> hide cartoons

> show cartoons

> hide atoms

> lighting shadows true

> lighting shadows false

> lighting simple

> select #1

29556 atoms, 32860 bonds, 34 pseudobonds, 1564 residues, 2 models selected  

> ui tool show "Color Actions"

> ui tool show "Color Actions"

> color sel royal blue

> color sel royal blue

> select clear

> open
> /yonath_group/disha/Gingivalis/delta266/models/comparision/RNA/23S_7k00_aligned_d266_30s-coot-0.pdb

Chain information for 23S_7k00_aligned_d266_30s-coot-0.pdb #2  
---  
Chain | Description  
A | No description available  
  

> hide atoms

> select #2

34830 atoms, 36578 bonds, 4 pseudobonds, 3678 residues, 2 models selected  

> color sel sea green

> color sel dark orange

> select clear

> close session

> open
> /yonath_group/disha/Gingivalis/delta266/models/comparision/RNA/16S_merged_FR_30S_D266_real_space_refined-
> coot-5.pdb

Chain information for 16S_merged_FR_30S_D266_real_space_refined-coot-5.pdb #1  
---  
Chain | Description  
a | No description available  
  

> select clear

> hide atoms

> color royal blue

> open
> /yonath_group/disha/Gingivalis/delta266/models/comparision/RNA/16S_7k00_aligned_d266_30s-coot-0.pdb

Chain information for 16S_7k00_aligned_d266_30s-coot-0.pdb #2  
---  
Chain | Description  
A | No description available  
  

> hide atoms

> select #2

34830 atoms, 36578 bonds, 4 pseudobonds, 3678 residues, 2 models selected  

> color sel dark orange

> select clear

> select clear

> select #1/a:204

20 atoms, 21 bonds, 1 residue, 1 model selected  

> color sel dim gray

> ui tool show Matchmaker

> matchmaker #!2 to #1 matrix Nucleic

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
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 16S_merged_FR_30S_D266_real_space_refined-coot-5.pdb, chain a (#1)
with 16S_7k00_aligned_d266_30s-coot-0.pdb, chain A (#2), sequence alignment
score = 3392.4  
RMSD between 605 pruned atom pairs is 1.339 angstroms; (across all 1350 pairs:
12.255)  
  

> open
> /yonath_group/disha/Gingivalis/delta266/models/comparision/RNA/16S_4w2e_aligned_d266_30s-coot-0.pdb

Chain information for 16S_4w2e_aligned_d266_30s-coot-0.pdb #3  
---  
Chain | Description  
a | No description available  
  

> color sel rosy brown

> select #3

32517 atoms, 36002 bonds, 4 pseudobonds, 1850 residues, 2 models selected  

> color sel rosy brown

> color sel dark olive green

> hide sel atoms

> undo

> hide sel atoms

> hide #!2 models

> hide #!3 models

> select #1/a: 1479-1485

133 atoms, 149 bonds, 6 residues, 1 model selected  

> select ~sel

96770 atoms, 105291 bonds, 42 pseudobonds, 7086 residues, 6 models selected  

> hide sel & #!1 cartoons

> select #1/a: 1479-1485

133 atoms, 149 bonds, 6 residues, 1 model selected  

> hide sel atoms

> show sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 133 atom styles  

> open
> /yonath_group/disha/Gingivalis/delta266/maps/3s_head_body_combined_aligned_shiny.mrc

Opened 3s_head_body_combined_aligned_shiny.mrc as #4, grid size 450,444,450,
pixel 0.852,0.852,0.852, shown at level 0.00558, step 2, values float32  

> volume #4 step 1

> volume #4 level 0.02

> volume step 2

> volume style mesh

> volume #4 color black

> volume #4 color #cacaca

> select #1/a: 1479-1485

133 atoms, 149 bonds, 6 residues, 1 model selected  

> ui tool show "Surface Zone"

> surface zone #4 nearAtoms sel distance 5.11

> surface zone #4 nearAtoms sel distance 10.67

> close #1

> open
> /yonath_group/disha/Gingivalis/delta266/models/comparision/RNA/16S_merged_FR_30S_D266_real_space_refined-
> coot-5.pdb

Chain information for 16S_merged_FR_30S_D266_real_space_refined-coot-5.pdb #1  
---  
Chain | Description  
a | No description available  
  

> hide #!1 atoms

> select #1

29556 atoms, 32860 bonds, 34 pseudobonds, 1564 residues, 2 models selected  

> hide sel cartoons

> select #1/a: 1479-1485

133 atoms, 149 bonds, 6 residues, 1 model selected  

> show sel cartoons

> show sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 133 atom styles  

> surface zone #4 nearAtoms sel distance 6.46

> open
> /yonath_group/disha/Gingivalis/delta266/models/final_models/merged_FR_30S_D266_real_space_refined-
> coot-4.pdb

Chain information for merged_FR_30S_D266_real_space_refined-coot-4.pdb #5  
---  
Chain | Description  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
T | No description available  
a | No description available  
o | No description available  
  

> hide sel atoms

> select #5

44960 atoms, 48441 bonds, 56 pseudobonds, 3595 residues, 2 models selected  

> hide sel atoms

> select #5/a: 1479-1485

133 atoms, 149 bonds, 6 residues, 1 model selected  

> show sel cartoons

> show sel cartoons

> show sel cartoons

> show sel atoms

> show sel surfaces

> hide sel surfaces

> show sel atoms

> show sel atoms

> hide sel atoms

> show sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 133 atom styles  

> volume #4 step 1

> volume #4 level 0.02056

> volume #4 level 0.003504

> select #5/a: 1479-1485

133 atoms, 149 bonds, 6 residues, 1 model selected  

> surface zone #4 nearAtoms sel distance 6.46

> surface zone #4 nearAtoms sel distance 6.46

> surface zone #4 nearAtoms sel distance 6.46

> surface zone #4 nearAtoms sel distance 6.46

> surface zone #4 nearAtoms sel distance 1.65

> volume step 1 subdivideSurface true

> surface zone #4 nearAtoms sel distance 2.12

> surface zone #4 nearAtoms sel distance 1.81

> close session

> open
> /yonath_group/disha/Gingivalis/delta266/models/final_models/merged_FR_30S_D266_real_space_refined-
> coot-4.pdb

Chain information for merged_FR_30S_D266_real_space_refined-coot-4.pdb #1  
---  
Chain | Description  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
T | No description available  
a | No description available  
o | No description available  
  

> hide cartoons

> show cartoons

> hide atoms

> open
> /yonath_group/disha/Gingivalis/delta266/models/comparision/4w2e_aligned_d266_30s.pdb

Chain information for 4w2e_aligned_d266_30s.pdb #2  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
8 | No description available  
9 | No description available  
A | No description available  
B | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
J | No description available  
K | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
  

> show cartoons

> hide atoms

> select #2/A-Z

88492 atoms, 95142 bonds, 1256 pseudobonds, 7400 residues, 3 models selected  

> hide sel cartoons

> select #2/1-8

4241 atoms, 4287 bonds, 15 pseudobonds, 539 residues, 2 models selected  

> hide sel cartoons

Drag select of 293 residues  

> select clear

Drag select of 85 residues  

> select clear

Drag select of 116 residues  

> hide sel cartoons

> lighting shadows false

> select clear

> open
> /yonath_group/disha/Gingivalis/delta266/models/comparision/4w2e_aligned_d266_30s.pdb

Chain information for 4w2e_aligned_d266_30s.pdb #3  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
8 | No description available  
9 | No description available  
A | No description available  
B | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
J | No description available  
K | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
  

> hide atoms

> show cartoons

> select #3/A-Z

88492 atoms, 95142 bonds, 1256 pseudobonds, 7400 residues, 3 models selected  

> hide sel cartoons

> close #3

> undo

Undo failed, probably because structures have been modified.  

> select #2/A-Z

88492 atoms, 95142 bonds, 1256 pseudobonds, 7400 residues, 3 models selected  

> hide sel cartoons

> select #2/1-8

4241 atoms, 4287 bonds, 15 pseudobonds, 539 residues, 2 models selected  

> hide sel cartoons

> open
> /yonath_group/disha/Gingivalis/delta266/models/comparision/7k00_aligned_d266_30s.pdb

Chain information for 7k00_aligned_d266_30s.pdb #3  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> hide sel atoms

> hide sel atoms

> hide sel atoms

> show sel cartoons

> select #3

149338 atoms, 154090 bonds, 1515 pseudobonds, 17719 residues, 3 models
selected  

> hide sel atoms

> show sel cartoons

> select #3/A-Z

57623 atoms, 59725 bonds, 410 pseudobonds, 6581 residues, 3 models selected  

> select #3/a-z

89518 atoms, 92211 bonds, 1092 pseudobonds, 10802 residues, 3 models selected  

> hide sel cartoons

Drag select of 328 residues  

> hide sel cartoons

Drag select of 363 residues  

> hide sel cartoons

Drag select of 73 residues  

> hide sel cartoons

> select all

346409 atoms, 365571 bonds, 3229 pseudobonds, 34413 residues, 8 models
selected  

> hide sel cartoons

> select #1/B

Nothing selected  

> select #1/C

1070 atoms, 1078 bonds, 12 pseudobonds, 142 residues, 2 models selected  

> show sel cartoons

> select #2/B

2625 atoms, 2878 bonds, 37 pseudobonds, 172 residues, 2 models selected  

> show sel cartoons

> select #2/b

1850 atoms, 1885 bonds, 231 residues, 1 model selected  

> show sel cartoons

> select #2/C

Nothing selected  

> select #2/c

1550 atoms, 1574 bonds, 206 residues, 1 model selected  

> show sel cartoons

> select #3/c

2183 atoms, 2121 bonds, 2 pseudobonds, 372 residues, 2 models selected  

> show sel cartoons

> select #3

149338 atoms, 154090 bonds, 1515 pseudobonds, 17719 residues, 3 models
selected  

> show sel cartoons

> hide sel cartoons

> select #3/C

1670 atoms, 1651 bonds, 252 residues, 1 model selected  

> show sel cartoons

> ui tool show Matchmaker

> matchmaker #!2 to #1 matrix Nucleic

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
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 merged_FR_30S_D266_real_space_refined-coot-4.pdb, chain a (#1) with
4w2e_aligned_d266_30s.pdb, chain a (#2), sequence alignment score = 3375.9  
RMSD between 584 pruned atom pairs is 1.307 angstroms; (across all 1352 pairs:
6.372)  
  

> ui tool show Matchmaker

> matchmaker #!3 to #1 matrix Nucleic

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
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 merged_FR_30S_D266_real_space_refined-coot-4.pdb, chain a (#1) with
7k00_aligned_d266_30s.pdb, chain A (#3), sequence alignment score = 3392.4  
RMSD between 605 pruned atom pairs is 1.339 angstroms; (across all 1350 pairs:
12.255)  
  

> hide #!3 models

> hide #!2 models

> show #!2 models

> open
> /yonath_group/disha/Gingivalis/delta266/swissmodels/RPS3/Untitled_Project/models/01/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for model.pdb #4  
---  
Chain | Description  
8 | No description available  
  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 43785, resource id:
31503556, major code: 40 (TranslateCoords), minor code: 0  

> ui tool show Matchmaker

> matchmaker #4 to #1 matrix Nucleic

No chains in match structure model.pdb #4 compatible with Nucleic similarity
matrix  

> ui tool show Matchmaker

> matchmaker #4 to #1 matrix BLOSUM-30

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-30  
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 merged_FR_30S_D266_real_space_refined-coot-4.pdb, chain C (#1) with
model.pdb, chain 8 (#4), sequence alignment score = 694  
RMSD between 132 pruned atom pairs is 0.966 angstroms; (across all 142 pairs:
2.993)  
  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> ui tool show Matchmaker

> matchmaker #4 to #2 matrix BLOSUM-30

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-30  
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 4w2e_aligned_d266_30s.pdb, chain c (#2) with model.pdb, chain 8
(#4), sequence alignment score = 670.2  
RMSD between 186 pruned atom pairs is 0.990 angstroms; (across all 205 pairs:
1.282)  
  

> show #!3 models

> show #!1 models

> save
> /yonath_group/disha/Gingivalis/delta266/models/comparision/SSU/rps3_chaiN_C.cxs

——— End of log from Tue May 17 14:49:39 2022 ———

opened ChimeraX session  

> select all

348024 atoms, 367204 bonds, 3229 pseudobonds, 34619 residues, 9 models
selected  

> hide sel cartoons

> select #3/D

1654 atoms, 1665 bonds, 216 residues, 1 model selected  

> show sel cartoons

> select #1/D

1584 atoms, 1617 bonds, 200 residues, 1 model selected  

> show sel cartoons

> select #2/d

1663 atoms, 1697 bonds, 3 pseudobonds, 209 residues, 2 models selected  

> show sel cartoons

> ui tool show Matchmaker

> matchmaker #3/D to #1/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 merged_FR_30S_D266_real_space_refined-coot-4.pdb, chain D (#1) with
7k00_aligned_d266_30s.pdb, chain D (#3), sequence alignment score = 575.8  
RMSD between 171 pruned atom pairs is 0.855 angstroms; (across all 199 pairs:
2.363)  
  

> ui tool show Matchmaker

> matchmaker #2/d to #1/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 merged_FR_30S_D266_real_space_refined-coot-4.pdb, chain D (#1) with
4w2e_aligned_d266_30s.pdb, chain d (#2), sequence alignment score = 565.7  
RMSD between 175 pruned atom pairs is 0.856 angstroms; (across all 200 pairs:
1.609)  
  

> save
> /yonath_group/disha/Gingivalis/delta266/models/comparision/SSU/rps4_chaiN_D.cxs

> select clear

> select all

348024 atoms, 367204 bonds, 3229 pseudobonds, 34619 residues, 9 models
selected  

> hide sel cartoons

> select #3/E

1167 atoms, 1165 bonds, 171 residues, 1 model selected  

> show sel cartoons

> select #1/E

1109 atoms, 1122 bonds, 157 residues, 1 model selected  

> show sel cartoons

> select #2/e

1130 atoms, 1145 bonds, 1 pseudobond, 149 residues, 2 models selected  

> show sel cartoons

> ui tool show Matchmaker

> matchmaker #3/E to #1/E 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 merged_FR_30S_D266_real_space_refined-coot-4.pdb, chain E (#1) with
7k00_aligned_d266_30s.pdb, chain E (#3), sequence alignment score = 463  
RMSD between 149 pruned atom pairs is 0.841 angstroms; (across all 155 pairs:
1.174)  
  

> ui tool show Matchmaker

> matchmaker #2/e to #1/E 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 merged_FR_30S_D266_real_space_refined-coot-4.pdb, chain E (#1) with
4w2e_aligned_d266_30s.pdb, chain e (#2), sequence alignment score = 395.4  
RMSD between 142 pruned atom pairs is 1.029 angstroms; (across all 148 pairs:
1.170)  
  

> save
> /yonath_group/disha/Gingivalis/delta266/models/comparision/SSU/rps4_chaiN_E.cxs

> select all

348024 atoms, 367204 bonds, 3229 pseudobonds, 34619 residues, 9 models
selected  

> hide sel cartoons

> select #1/F

878 atoms, 894 bonds, 107 residues, 1 model selected  

> show sel cartoons

> show sel cartoons

> show sel cartoons

> view sel

> select #3/F

839 atoms, 858 bonds, 103 residues, 1 model selected  

> show sel cartoons

> select #2/f

807 atoms, 819 bonds, 1 pseudobond, 101 residues, 2 models selected  

> show sel cartoons

> ui tool show Matchmaker

> matchmaker #3/F to #1/F 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 merged_FR_30S_D266_real_space_refined-coot-4.pdb, chain F (#1) with
7k00_aligned_d266_30s.pdb, chain F (#3), sequence alignment score = 184.3  
RMSD between 64 pruned atom pairs is 0.839 angstroms; (across all 93 pairs:
3.521)  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/opt/UCSF/ChimeraX/lib/python3.8/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 "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> ui tool show Matchmaker

> matchmaker #2/f to #1/F 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 merged_FR_30S_D266_real_space_refined-coot-4.pdb, chain F (#1) with
4w2e_aligned_d266_30s.pdb, chain f (#2), sequence alignment score = 91.1  
RMSD between 79 pruned atom pairs is 1.065 angstroms; (across all 99 pairs:
3.309)  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/opt/UCSF/ChimeraX/lib/python3.8/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 "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  

> select clear

Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/opt/UCSF/ChimeraX/lib/python3.8/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 "/opt/UCSF/ChimeraX/lib/python3.8/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
> /yonath_group/disha/Gingivalis/delta266/models/comparision/SSU/rps6_chaiN_F.cxs

> select all

348024 atoms, 367204 bonds, 3229 pseudobonds, 34619 residues, 9 models
selected  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/opt/UCSF/ChimeraX/lib/python3.8/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 "/opt/UCSF/ChimeraX/lib/python3.8/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 sel cartoons

Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/opt/UCSF/ChimeraX/lib/python3.8/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 "/opt/UCSF/ChimeraX/lib/python3.8/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change  
if not hasattr(self, '_recursion'):  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 418.113
OpenGL renderer: Quadro RTX 4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUS
Model: System Product Name
OS: CentOS Stream 8 
Architecture: 64bit ELF
Virutal Machine: none
CPU: 24 AMD Ryzen 9 5900X 12-Core Processor
Cache Size: 512 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           62Gi        30Gi        20Gi       1.6Gi        12Gi        30Gi
	Swap:          31Gi       5.3Gi        26Gi

Graphics:
	05:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU104GL [Quadro RTX 4000] [10de:1eb1] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:12a0]	
	Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.4.1
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.3
    ChimeraX-AtomicLibrary: 3.1.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.1
    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: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    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: 1.2
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    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: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.3
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    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: 0.29.21
    decorator: 5.0.7
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 1.1.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    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: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.2.0

Change History (2)

comment:1 by pett, 3 years ago

Component:	Unassigned → Structure Comparison
Owner:	set to pett
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → MatchMaker: wrapped C/C++ object of type ChainMenuButton has been deleted

comment:2 by pett, 3 years ago

Resolution:	→ duplicate
Status:	accepted → closed

Hi Disha,

Thanks for reporting this problem. This problem has been fixed, so If you upgrade to any current version of ChimeraX you won't run into it anymore.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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