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#4416 closed defect (duplicate)

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

Reported by:	yuhang.wang.19@…	Owned by:	Eric Pettersen
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:        Windows-10-10.0.18362
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
Match maker (align two chains from two proteins)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> help help:quickstart

> help help:quickstart

Successfully installed ChimeraX-AddH-2.1.3 ChimeraX-HKCage-1.3  
Installed ChimeraX-AddH (2.1.3)  
Installed ChimeraX-HKCage (1.3)  

> open 3uag

Summary of feedback from opening 3uag fetched from pdb  
---  
warning | Unable to infer polymer connectivity due to unspecified label_seq_id
for residue "UMA" near line 4565  
notes | Fetching compressed mmCIF 3uag from
http://files.rcsb.org/download/3uag.cif  
Fetching CCD MN from http://ligand-expo.rcsb.org/reports/M/MN/MN.cif  
Fetching CCD UMA from http://ligand-expo.rcsb.org/reports/U/UMA/UMA.cif  
Fetching CCD ADP from http://ligand-expo.rcsb.org/reports/A/ADP/ADP.cif  
Fetching CCD EPE from http://ligand-expo.rcsb.org/reports/E/EPE/EPE.cif  
Fetching CCD KCX from http://ligand-expo.rcsb.org/reports/K/KCX/KCX.cif  
  
3uag title:  
UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase [more info...]  
  
Chain information for 3uag #1  
---  
Chain | Description  
A | protein (udp-N-acetylmuramoyl-L-alanine:D-glutamate ligase)  
  
Non-standard residues in 3uag #1  
---  
ADP — adenosine-5'-diphosphate  
EPE — 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES)  
MN — manganese (II) ion  
  

> lighting full

> style /b stick

Changed 0 atom styles  
Drag select of 32 atoms, 100 residues, 1 pseudobonds, 20 bonds  

> style /b stick

Changed 0 atom styles  

> select clear

> style /a stick

Changed 3686 atom styles  

> delete

Missing or invalid "atoms" argument: empty atom specifier  

> close #1

> open 7kkj

Summary of feedback from opening 7kkj fetched from pdb  
---  
notes | Fetching compressed mmCIF 7kkj from
http://files.rcsb.org/download/7kkj.cif  
Fetching CCD SO4 from http://ligand-expo.rcsb.org/reports/S/SO4/SO4.cif  
Fetching CCD CL from http://ligand-expo.rcsb.org/reports/C/CL/CL.cif  
  
7kkj title:  
Structure of anti-SARS-CoV-2 Spike nanobody mNb6 [more info...]  
  
Chain information for 7kkj #1  
---  
Chain | Description  
A C | Synthetic nanobody mNb6  
  
Non-standard residues in 7kkj #1  
---  
CL — chloride ion  
SO4 — sulfate ion  
  
7kkj mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> select :CL

1 atom, 1 residue, 1 model selected  

> select :SO4

20 atoms, 16 bonds, 4 residues, 1 model selected  

> select :CL

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> hide sel atoms

> select :CL

1 atom, 1 residue, 1 model selected  

> show sel atoms

> select :SO4

20 atoms, 16 bonds, 4 residues, 1 model selected  

> hide sel atoms

> show sel atoms

> sym #1 assembly 1

> view

> sym #1 assembly 2

> view

> sym #1 assembly 1

> view

> show #1 models

> hide #1 models

> hide #2 models

> hide #3 models

> show #3 models

> show #2 models

> hide #3 models

> show #3 models

> show #1 models

> hide #1 models

> close #2

> close #3

> close #4

> show #1 models

> select :CL

1 atom, 1 residue, 1 model selected  

> show sel atoms

> show sel atoms

> hide sel atoms

> show sel atoms

> show sel atoms

> hide sel atoms

> select clear

> show atoms

> hide atoms

> show atoms

> select clear

> hide atoms

> hide atoms

> show atoms

> hide atoms

> show atoms

> hide atoms

> select clear

> show atoms

> show atoms

> hide atoms

> clear

Unknown command: clear  
Drag select of 237 residues  

> hide sel cartoons

> show sel cartoons

> style sel stick

Changed 3531 atom styles  

> style sel sphere

Changed 3531 atom styles  

> show sel atoms

> style sel ball

Changed 3531 atom styles  

> style sel sphere

Changed 3531 atom styles  

> style sel stick

Changed 3531 atom styles  

> hide sel cartoons

> show sel cartoons

> hide sel cartoons

> show sel cartoons

> hide sel cartoons

> show sel cartoons

> style sel sphere

Changed 3531 atom styles  

> style sel stick

Changed 3531 atom styles  

> style sel ball

Changed 3531 atom styles  

> close

> open 3uag format mmcif fromDatabase pdb

Summary of feedback from opening 3uag fetched from pdb  
---  
warning | Unable to infer polymer connectivity due to unspecified label_seq_id
for residue "UMA" near line 4565  
  
3uag title:  
UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase [more info...]  
  
Chain information for 3uag #1  
---  
Chain | Description  
A | protein (udp-N-acetylmuramoyl-L-alanine:D-glutamate ligase)  
  
Non-standard residues in 3uag #1  
---  
ADP — adenosine-5'-diphosphate  
EPE — 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES)  
MN — manganese (II) ion  
  

> show atoms

> hide atoms

> show atoms

> show cartoons

> hide cartoons

> style stick

Changed 3686 atom styles  

> style sphere

Changed 3686 atom styles  

> style ball

Changed 3686 atom styles  

> style sphere

Changed 3686 atom styles  

> open 3uag

Summary of feedback from opening 3uag fetched from pdb  
---  
warning | Unable to infer polymer connectivity due to unspecified label_seq_id
for residue "UMA" near line 4565  
  
3uag title:  
UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase [more info...]  
  
Chain information for 3uag #2  
---  
Chain | Description  
A | protein (udp-N-acetylmuramoyl-L-alanine:D-glutamate ligase)  
  
Non-standard residues in 3uag #2  
---  
ADP — adenosine-5'-diphosphate  
EPE — 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES)  
MN — manganese (II) ion  
  

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> lighting soft

> lighting simple

> lighting full

> lighting full

> lighting soft

> hide #!1 atoms

> hide #!1 atoms

> show #!1 atoms

> style #!1 stick

Changed 3686 atom styles  

> show #!1 cartoons

> hide #!1 cartoons

> show #!1 cartoons

> hide #!1 atoms

> lighting full

> select #1/A:424

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

> select #1/A:343

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

> select #1/A:343

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

> select #1/A:344

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #1/A:343

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

> select up

46 atoms, 46 bonds, 6 residues, 1 model selected  

> select down

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

> select down

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

> select up

46 atoms, 46 bonds, 6 residues, 1 model selected  

> select up

3686 atoms, 3383 bonds, 793 residues, 1 model selected  

> select #1/A:120

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

> select up

98 atoms, 97 bonds, 14 residues, 1 model selected  

> color sel yellow

> select #1/A:367

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select up

55 atoms, 56 bonds, 6 residues, 1 model selected  

> select up

3686 atoms, 3383 bonds, 793 residues, 1 model selected  

> select down

55 atoms, 56 bonds, 6 residues, 1 model selected  

> color sel bychain

> color sel bychain

> rainbow sel

> color sel byhetero

> coulombic sel

Don't know how to assign charges to the following residue types: KCX  

> mlp sel

Map values for surface "3uag_A SES surface": minimum -29.38, mean -6.019,
maximum 71.59  

> color bfactor sel

55 atoms, 6 residues, 1 surfaces, atom bfactor range 14 to 46.7  

> color bfactor sel

55 atoms, 6 residues, 1 surfaces, atom bfactor range 14 to 46.7  

> color sel bynucleotide

> color sel byhetero

> color sel bychain

> color sel byhetero

> select clear

> color #!1 bychain

> color #!1 byhetero

> rainbow #!1

> coulombic #!1

Don't know how to assign charges to the following residue types: KCX  

> mlp #!1

Map values for surface "3uag_A SES surface": minimum -6.634e+05, mean -823.8,
maximum 22.21  

> color #!1 byhetero

> rainbow #!1

> mlp #!1

Map values for surface "3uag_A SES surface": minimum -29.38, mean -6.128,
maximum 22.21  

> rainbow #!1

> hide #!1 atoms

> hide #!1 atoms

> select clear

> hide #!1 atoms

> show #!1 atoms

> show #!1 cartoons

> hide #!1 cartoons

> hide #!1 surfaces

> show #!1 cartoons

> hide #!1 atoms

> color #!1 byhetero

> select clear

> color #!1 byhetero

> color #!1 byhetero

> rainbow #!1

> rainbow #!1

> hide #!1 atoms

> preset "initial styles" "original look"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> lighting soft

> preset cartoons/nucleotides cylinders/stubs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> select clear

> ui tool show ViewDockX

No suitable models found for ViewDockX  

> show #!1 surfaces

> hide #!1 surfaces

> show #!1 surfaces

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

15 atoms, 15 bonds, 1 residue, 1 model selected  

> delete elected

Missing or invalid "atoms" argument: invalid atoms specifier  

> coulombic sel

Don't know how to assign charges to the following residue types: EPE  

> select clear

Drag select of 3uag_A SES surface, 324486 of 324758 triangles, 92 atoms, 470
residues, 3 pseudobonds, 95 bonds  

> coulombic sel

Don't know how to assign charges to the following residue types: KCX  

> delete H

> coulombic sel

Don't know how to assign charges to the following residue types: KCX  
Drag select of 3uag_A SES surface, 18939 of 324758 triangles, 26 atoms, 59
residues, 28 bonds  

> select clear

Drag select of 3uag_A SES surface, 92 atoms, 470 residues, 3 pseudobonds, 95
bonds  

> coulombic sel

Don't know how to assign charges to the following residue types: KCX  
Drag select of 3uag_A SES surface, 92 atoms, 470 residues, 3 pseudobonds, 95
bonds  

> delete H

> coulombic sel

Don't know how to assign charges to the following residue types: KCX  

> open 7kkj

7kkj title:  
Structure of anti-SARS-CoV-2 Spike nanobody mNb6 [more info...]  
  
Chain information for 7kkj #3  
---  
Chain | Description  
A C | Synthetic nanobody mNb6  
  
Non-standard residues in 7kkj #3  
---  
CL — chloride ion  
SO4 — sulfate ion  
  
7kkj mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> hide #1.3 models

> hide #1.2 models

> hide #1.1 models

> hide #!1 models

> lighting soft

> delete H

> show #3 surfaces

> coulombic #!3

The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics: 7kkj #3/C SER 119 OG  

> mlp #!3

Map values for surface "7kkj_A SES surface": minimum -26.2, mean -6.038,
maximum 19.75  
Map values for surface "7kkj_C SES surface": minimum -25.35, mean -5.999,
maximum 20.09  

> coulombic #!3

> open 4uag

Summary of feedback from opening 4uag fetched from pdb  
---  
notes | Fetching compressed mmCIF 4uag from
http://files.rcsb.org/download/4uag.cif  
Fetching CCD UAG from http://ligand-expo.rcsb.org/reports/U/UAG/UAG.cif  
Fetching CCD UNX from http://ligand-expo.rcsb.org/reports/U/UNX/UNX.cif  
  
4uag title:  
UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase [more info...]  
  
Chain information for 4uag #4  
---  
Chain | Description  
A | udp-N-acetylmuramoyl-L-alanine:D-glutamate ligase  
  
Non-standard residues in 4uag #4  
---  
SO4 — sulfate ion  
UAG — uridine-5'-diphosphate-N-acetylmuramoyl-L-alanine-D-glutamate  
UNX — unknown atom or ion  
  

> hide #!3 models

> delete H

> show #!4 surfaces

> coulombic #!4

Don't know how to assign charges to the following residue types: KCX  

> delete KCK

Missing or invalid "atoms" argument: invalid atoms specifier  

> color bfactor #!4

3623 atoms, 761 residues, 1 surfaces, atom bfactor range 5.94 to 63.8  

> show #!2 models

> hide #!4 models

> hide #4.1 models

> hide #4.2 models

> mlp #!2

Map values for surface "3uag_A SES surface": minimum -29.38, mean -6.128,
maximum 22.21  

> color #!2 byhetero

> color #!2 bychain

> rainbow #!2

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A #2/A #4/A

Alignment identifier is 1  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

15 atoms, 15 bonds, 1 residue, 1 model selected  
Seqview [ID: 1] region 3 chains [168-180] RMSD: 0.306  
  

> hide sel & #!2 surfaces

> hide sel & #!2 surfaces

> show sel & #!2 surfaces

> ui tool show "Modeller Comparative"

> open 4uag fromDatabase eds

Summary of feedback from opening 4uag fetched from eds  
---  
note | Fetching map 4uag from
http://www.ebi.ac.uk/pdbe/coordinates/files/4uag.ccp4  
  
Opened 4uag.ccp4, grid size 140,118,116, pixel 0.548,0.548,0.561, shown at
level 1.19, step 1, values float32  

> volume #5 level 1.198

> style sel & #!2 stick

Changed 90 atom styles  

> select clear

> style #!2 stick

Changed 3686 atom styles  

> hide #!2 surfaces

> volume #5 level 0.8919

> volume #5 level 0.6055

> volume #5 level 0.803

> volume #5 color #ff55ff

> volume #5 color #aaff7f

> volume #5 color white

> volume showOutlineBox true

> volume zone #2 nearAtoms #1

> ui tool show "Side View"

> volume showOutlineBox false

> hide #!2 models

> hide #!5 models

> show #!4 models

> ui tool show "Modeller Comparative"

No alignments chosen for modeling  
Drag select of 206 atoms, 429 residues, 158 bonds  

> ui tool show "Modeller Comparative"

No alignments chosen for modeling  

> open 7kkl

Summary of feedback from opening 7kkl fetched from pdb  
---  
notes | Fetching compressed mmCIF 7kkl from
http://files.rcsb.org/download/7kkl.cif  
Fetching CCD NAG from http://ligand-expo.rcsb.org/reports/N/NAG/NAG.cif  
  
7kkl title:  
SARS-CoV-2 Spike in complex with neutralizing nanobody mNb6 [more info...]  
  
Chain information for 7kkl #6  
---  
Chain | Description  
A C D | Spike glycoprotein  
B E F | Synthetic nanobody mNb6  
  
Non-standard residues in 7kkl #6  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  

> open 7kkl

7kkl title:  
SARS-CoV-2 Spike in complex with neutralizing nanobody mNb6 [more info...]  
  
Chain information for 7kkl #7  
---  
Chain | Description  
A C D | Spike glycoprotein  
B E F | Synthetic nanobody mNb6  
  
Non-standard residues in 7kkl #7  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  

> hide #!4 models

> hide #!6 models

> select #7

53325 atoms, 54012 bonds, 21 pseudobonds, 3423 residues, 2 models selected  

> ~select #7

Nothing selected  

> hide #!7 models

> close

> open 7kkl

7kkl title:  
SARS-CoV-2 Spike in complex with neutralizing nanobody mNb6 [more info...]  
  
Chain information for 7kkl #1  
---  
Chain | Description  
A C D | Spike glycoprotein  
B E F | Synthetic nanobody mNb6  
  
Non-standard residues in 7kkl #1  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  

> select /B:13@HG3

1 atom, 1 residue, 1 model selected  

> select up

52 atoms, 50 bonds, 3 residues, 1 model selected  

> select up

355 atoms, 354 bonds, 22 residues, 1 model selected  

> select up

5256 atoms, 5313 bonds, 354 residues, 1 model selected  

> color sel yellow

> color /B,E,F gold

> color /B,E,F red

Drag select of 53325 atoms, 21 pseudobonds, 1809 bonds  

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> save C:\Users\10749\Desktop\image1.png supersample 3

> save C:\Users\10749\Desktop\image2.png supersample 3

> open 3uag format mmcif fromDatabase pdb

Summary of feedback from opening 3uag fetched from pdb  
---  
warning | Unable to infer polymer connectivity due to unspecified label_seq_id
for residue "UMA" near line 4565  
  
3uag title:  
UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase [more info...]  
  
Chain information for 3uag #2  
---  
Chain | Description  
A | protein (udp-N-acetylmuramoyl-L-alanine:D-glutamate ligase)  
  
Non-standard residues in 3uag #2  
---  
ADP — adenosine-5'-diphosphate  
EPE — 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES)  
MN — manganese (II) ion  
  

> save C:\Users\10749/Deskspike.png width 1500

> open 6vxx

Summary of feedback from opening 6vxx fetched from pdb  
---  
note | Fetching compressed mmCIF 6vxx from
http://files.rcsb.org/download/6vxx.cif  
  
6vxx title:  
Structure of the SARS-CoV-2 spike glycoprotein (closed state) [more info...]  
  
Chain information for 6vxx #3  
---  
Chain | Description  
A B C | Spike glycoprotein  
  
Non-standard residues in 6vxx #3  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  

> select clear

> select #1/C:533@HB2

1 atom, 1 residue, 1 model selected  

> select up

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select up

197 atoms, 197 bonds, 12 residues, 1 model selected  

> select up

15693 atoms, 15891 bonds, 1011 residues, 1 model selected  

> select up

53325 atoms, 54012 bonds, 3423 residues, 1 model selected  

> select up

80705 atoms, 81692 bonds, 7195 residues, 3 models selected  

> select up

80705 atoms, 81692 bonds, 7195 residues, 3 models selected  

> select down

53325 atoms, 54012 bonds, 3423 residues, 1 model selected  

> select clear

> select #3/A:594

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select up

54 atoms, 54 bonds, 8 residues, 1 model selected  

> select up

7758 atoms, 7949 bonds, 983 residues, 1 model selected  

> select up

23694 atoms, 24297 bonds, 2979 residues, 1 model selected  

> hide sel cartoons

> show sel atoms

> color sel byhetero

> show sel surfaces

> color sel byhetero

> select up

23694 atoms, 24297 bonds, 33 pseudobonds, 2979 residues, 5 models selected  

> select #1/C:533@CD2

1 atom, 1 residue, 1 model selected  

> select up

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select up

197 atoms, 197 bonds, 12 residues, 1 model selected  

> select up

15693 atoms, 15891 bonds, 1011 residues, 1 model selected  

> select up

53325 atoms, 54012 bonds, 3423 residues, 1 model selected  

> color bfactor sel

53325 atoms, 3423 residues, atom bfactor range 62.3 to 225  

> color sel bychain

> color sel byhetero

> color sel bynucleotide

> coulombic sel

> ui mousemode right "translate selected models"

> select clear

> select #1/C:643@CD1

1 atom, 1 residue, 1 model selected  

> select up

20 atoms, 20 bonds, 1 residue, 2 models selected  

> select up

67 atoms, 67 bonds, 4 residues, 2 models selected  

> select up

15693 atoms, 15891 bonds, 1011 residues, 2 models selected  

> select up

53325 atoms, 54012 bonds, 3423 residues, 2 models selected  

> select up

53325 atoms, 54012 bonds, 21 pseudobonds, 3423 residues, 8 models selected  
Drag select of 7kkl_A SES surface, 3397 of 1157934 triangles, 7kkl_C SES
surface, 9957 of 1158332 triangles, 7kkl_D SES surface, 2716 of 1152598
triangles, 156 atoms  

> select up

683 atoms, 664 bonds, 45 residues, 4 models selected  

> select up

3074 atoms, 3078 bonds, 202 residues, 4 models selected  

> select up

47079 atoms, 47673 bonds, 3033 residues, 4 models selected  

> select up

53325 atoms, 54012 bonds, 3423 residues, 4 models selected  

> ui mousemode right "translate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right "translate selected models"

Drag select of 7kkl_A SES surface, 11916 of 1157934 triangles, 7kkl_C SES
surface, 22810 of 1158332 triangles, 7kkl_D SES surface, 25555 of 1152598
triangles, 853 atoms, 2 bonds  

> ui tool show "Fit in Map"

> select #3/C:440@O

1 atom, 1 residue, 1 model selected  

> select #1

53325 atoms, 54012 bonds, 21 pseudobonds, 3423 residues, 2 models selected  

> select #2

3686 atoms, 3383 bonds, 8 pseudobonds, 793 residues, 3 models selected  

> select #3

23694 atoms, 24297 bonds, 33 pseudobonds, 2979 residues, 2 models selected  

> select #2

3686 atoms, 3383 bonds, 8 pseudobonds, 793 residues, 3 models selected  

> open 7kkj

7kkj title:  
Structure of anti-SARS-CoV-2 Spike nanobody mNb6 [more info...]  
  
Chain information for 7kkj #4  
---  
Chain | Description  
A C | Synthetic nanobody mNb6  
  
Non-standard residues in 7kkj #4  
---  
CL — chloride ion  
SO4 — sulfate ion  
  
7kkj mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> select #4/C

1841 atoms, 1792 bonds, 187 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> undo

Undo failed, probably because structures have been modified.  

> undo

> undo

> undo

> undo

> undo

> ui tool show Matchmaker

> matchmaker #4/A to #1/B 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 7kkl, chain B (#1) with 7kkj, chain A (#4), sequence alignment
score = 589.7  
RMSD between 90 pruned atom pairs is 0.751 angstroms; (across all 117 pairs:
3.062)  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\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 "C:\Program Files\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.  
  

> mmaker #4/A to #1/B

Parameters  
---  
Chain pairing | bb  
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 7kkl, chain B (#1) with 7kkj, chain A (#4), sequence alignment
score = 589.7  
RMSD between 90 pruned atom pairs is 0.751 angstroms; (across all 117 pairs:
3.062)  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\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 "C:\Program Files\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.  
  

> select #1/A:245@CG

1 atom, 1 residue, 1 model selected  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\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 "C:\Program Files\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.  
  

> select #1/A:607@N

1 atom, 1 residue, 1 model selected  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\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 "C:\Program Files\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.  
  




OpenGL version: 3.3.13559 Core Profile Forward-Compatible Context 26.20.12036.1
OpenGL renderer: Radeon (TM) 540X
OpenGL vendor: ATI Technologies Inc.
Manufacturer: LENOVO
Model: 20QC000HCD
OS: Microsoft Windows 10 家庭中文版 (Build 18363)
Memory: 8,395,395,072
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-8265U CPU @ 1.60GHz"
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

Change History (2)

comment:1 by Eric Pettersen, 5 years ago

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

comment:2 by Eric Pettersen, 5 years ago

Resolution:	→ duplicate
Status:	accepted → closed

Hi Yuhang,

Thanks for reporting this problem. We believe this issue has been fixed in the daily build, so please use that if you'd like to avoid this problem in the future.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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