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#15848 closed defect (can't reproduce)

Crash in event loop

Reported by:	745324914@…	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	Core	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x8001010d

Current thread 0x0000cb3c (most recent call first):
  File "D:\software\install\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "D:\software\install\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "D:\software\install\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "D:\software\install\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "D:\software\install\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
> open D:\PhD\Nannochloropsis_oceanica\session\NO.cxs format session

opened ChimeraX session  

> open D:/PhD/Nannochloropsis_oceanica/mrc/2.89Aoverall.mrc

Opened 2.89Aoverall.mrc as #2, grid size 440,440,440, pixel 1.06, shown at
level 0.0212, step 2, values float32  

> volume #2 level 0.05857

> volume #2 step 1

> volume #2 level 0.08084

> save D:/PhD/Nannochloropsis_oceanica/session/NO.cxs

> volume zone #2 nearAtoms sel #1:801

Expected a keyword  

> ui tool show "Model Panel"

> ui tool show "File History"

> ui tool show Log

> volume zone #2 nearAtoms #1/A:801

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> set bgColor black

> set bgColor white

> hide #!1 models

> select /A

8862 atoms, 9231 bonds, 200 pseudobonds, 795 residues, 2 models selected  

> show #!1 models

> show sel atoms

> hide sel cartoons

> hide #!1 models

> volume #2 level 0.06235

> volume #2 level 0.04633

> volume #2 level 0.07468

> surface style mesh

> volume #2 level 0.06728

> hide #!2 models

> show #!2 models

> show #!1 models

> hide #!1 models

> hide #!2 models

> show #!2 models

> select #2

2 models selected  

> ~select #2

Nothing selected  

> hide #!2 models

> show #!1 models

> select #1

44542 atoms, 46271 bonds, 1024 pseudobonds, 4149 residues, 3 models selected  

> ~select #1

Nothing selected  

> select #1/A:801

65 atoms, 69 bonds, 4 pseudobonds, 1 residue, 2 models selected  

> save D:/PhD/Nannochloropsis_oceanica/cif/chla801A.pdb selectedOnly true
> relModel #1

> open D:/PhD/Nannochloropsis_oceanica/cif/chla801A.pdb

Summary of feedback from opening
D:/PhD/Nannochloropsis_oceanica/cif/chla801A.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 LYS A 21
ALA A 23 1 3  
Start residue of secondary structure not found: HELIX 2 2 LEU A 32 LYS A 34 1
3  
Start residue of secondary structure not found: HELIX 3 3 THR A 39 ALA A 47 1
9  
Start residue of secondary structure not found: HELIX 4 4 PHE A 52 GLN A 55 1
4  
Start residue of secondary structure not found: HELIX 5 5 LEU A 59 TYR A 90 1
32  
176 messages similar to the above omitted  
Cannot find LINK/SSBOND residue CYS (32 )  
Cannot find LINK/SSBOND residue GLU (151 )  
Cannot find LINK/SSBOND residue BCR (845 )  
Cannot find LINK/SSBOND residue CLA (810 )  
Cannot find LINK/SSBOND residue CLA (832 )  
187 messages similar to the above omitted  
  

> hide #!1 models

> show #!2 models

> hide #!2 models

> open D:/PhD/Nannochloropsis_oceanica/mrc/sharpen_combine.mrc

Opened sharpen_combine.mrc as #4, grid size 440,440,440, pixel 1.06, shown at
level 0.000234, step 2, values float32  

> volume #4 level 0.1856

> volume #4 step 1

> show #!2 models

> hide #!2 models

> hide #!4 models

> select #1

44542 atoms, 46271 bonds, 1024 pseudobonds, 4149 residues, 3 models selected  

> volume zone #4 nearAtoms #3

> show #!4 models

> volume #4 level 0.2212

> surface style #4 mesh

> volume #4 level 0.3139

> surface style #4 mesh

> volume #4 level 0.07864

> surface style #4 mesh

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

> select #4

2 models selected  

> select #3

65 atoms, 69 bonds, 4 pseudobonds, 1 residue, 2 models selected  

> hide #!4 models

> close #3

> open "D:/PhD/Nannochloropsis_oceanica/other algae/8jzeSs.pdb"
> "D:/PhD/Nannochloropsis_oceanica/other algae/8jzfSs.pdb"

8jzeSs.pdb title:  
Psi-acppci supercomplex from symbiodinium [more info...]  
  
Chain information for 8jzeSs.pdb #3  
---  
Chain | Description  
A | chlorophyll A-chlorophyll C-peridinin-protein-complex I-10, acppci-10  
B | chlorophyll A-chlorophyll C-peridinin-protein-complex I-11, acppci-11  
D | chlorophyll A-chlorophyll C-peridinin-protein-complex I-9, acppci-9  
F | chlorophyll A-chlorophyll C-peridinin-protein-complex I-2, acppci-2  
G | chlorophyll A-chlorophyll C-peridinin-protein-complex I-8, acppci-8  
H | chlorophyll A-chlorophyll C-peridinin-protein-complex I-12, acppci-12  
I | chlorophyll A-chlorophyll C-peridinin-protein-complex I-7, acppci-7  
J | chlorophyll A-chlorophyll C-peridinin-protein-complex I-3, acppci-3  
K | chlorophyll A-chlorophyll C-peridinin-protein-complex I-6, acppci-6  
L | chlorophyll A-chlorophyll C-peridinin-protein-complex I-5, acppci-5  
M | chlorophyll A-chlorophyll C-peridinin-protein-complex I-4, acppci-4  
N | chlorophyll A-chlorophyll C-peridinin-protein-complex I-13, acppci-13  
O | chlorophyll A-chlorophyll C-peridinin-protein-complex I-15, acppci-15  
P | chlorophyll A-chlorophyll C-peridinin-protein-complex I-14, acppci-14  
a | photosystem I psaa  
b | photosystem I psab  
c | photosystem I psac  
d | photosystem I psad  
e | photosystem I psae  
f | photosystem I psaf  
h | photosystem I psar  
i | photosystem I psai  
j | photosystem I psaj  
l | photosystem I psal  
m | photosystem I psam  
y | photosystem I unk  
z | photosystem I unk  
  
Non-standard residues in 8jzeSs.pdb #3  
---  
BCR — β-carotene  
CLA — chlorophyll A  
DD6 —
(3S,3'R,5R,6S,7CIS)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-β,β-carotene-3,3'-diol
(diadinoxanthin)  
DGD — digalactosyl diacyl glycerol (DGDG)  
KC1 — chlorophyll C1  
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole  
LMG — 1,2-distearoyl-monogalactosyl-diglyceride  
PID — peridinin  
PQN — phylloquinone (vitamin K1; 2-methyl-3-phytyl-1,4-naphthoquinone)  
SF4 — iron/sulfur cluster  
SQD — 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-α-D-glucopyranosyl]-Sn-glycerol
(sulfoquinovosyldiacylglycerol)  
UIX —
[(1~{S},5~{R})-3,3,5-trimethyl-5-oxidanyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenylidene]cyclohexyl]
ethanoate (dinoxanthin)  
  
8jzfSs.pdb title:  
Psi-acppci supercomplex from symbiodinium [more info...]  
  
Chain information for 8jzfSs.pdb #5  
---  
Chain | Description  
A | chlorophyll A-chlorophyll C-peridinin-protein-complex I-10, acppci-10  
B | chlorophyll A-chlorophyll C-peridinin-protein-complex I-11, acppci-11  
D | chlorophyll A-chlorophyll C-peridinin-protein-complex I-9, acppci-9  
F | chlorophyll A-chlorophyll C-peridinin-protein-complex I-2, acppci-2  
G | chlorophyll A-chlorophyll C-peridinin-protein-complex I-8, acppci-8  
H | chlorophyll A-chlorophyll C-peridinin-protein-complex I-12, acppci-12  
I | chlorophyll A-chlorophyll C-peridinin-protein-complex I-7, acppci-7  
J | chlorophyll A-chlorophyll C-peridinin-protein-complex I-3, acppci-3  
K | chlorophyll A-chlorophyll C-peridinin-protein-complex I-6, acppci-6  
L | chlorophyll A-chlorophyll C-peridinin-protein-complex I-5, acppci-5  
M | chlorophyll A-chlorophyll C-peridinin-protein-complex I-4, acppci-4  
N | chlorophyll A-chlorophyll C-peridinin-protein-complex I-13, acppci-13  
a | photosystem I psaa  
b | photosystem I psab  
c | photosystem I psac  
d | photosystem I psad  
e | photosystem I psae  
f | photosystem I psaf  
h | photosystem I psar  
i | photosystem I psai  
j | photosystem I psaj  
l | photosystem I psal  
m | photosystem I psam  
y | photosystem I unk  
z | photosystem I unk  
  
Non-standard residues in 8jzfSs.pdb #5  
---  
BCR — β-carotene  
CLA — chlorophyll A  
DD6 —
(3S,3'R,5R,6S,7CIS)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-β,β-carotene-3,3'-diol
(diadinoxanthin)  
DGD — digalactosyl diacyl glycerol (DGDG)  
KC1 — chlorophyll C1  
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole  
LMG — 1,2-distearoyl-monogalactosyl-diglyceride  
PID — peridinin  
PQN — phylloquinone (vitamin K1; 2-methyl-3-phytyl-1,4-naphthoquinone)  
SF4 — iron/sulfur cluster  
SQD — 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-α-D-glucopyranosyl]-Sn-glycerol
(sulfoquinovosyldiacylglycerol)  
UIX —
[(1~{S},5~{R})-3,3,5-trimethyl-5-oxidanyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenylidene]cyclohexyl]
ethanoate (dinoxanthin)  
  

> hide #!3,5 atoms

> show #!3,5 cartoons

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> hide #!3 models

> show #!3 models

> show #!5 models

> hide #!3 models

> show #!3 models

> close #5

> show #!1 models

> hide #!1 models

> show #!1 models

> ui tool show Matchmaker

> matchmaker #!3 to #1

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 NO0828.pdb, chain A (#1) with 8jzeSs.pdb, chain a (#3), sequence
alignment score = 1993.6  
RMSD between 579 pruned atom pairs is 0.766 angstroms; (across all 656 pairs:
3.436)  
  

> hide #!1 models

> show #!1 models

> hide #!3 models

> hide #!1 atoms

> show #!1 cartoons

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> color #1 forest green

> color #1 yellow

> cartoon style #1 modeHelix tube sides 20

> show #!3 models

> color #1,3 cyan

> hide #!1 models

> show #!1 models

> color #3 #ff5500 transparency 0

> cartoon style #1,3 modeHelix tube sides 20

> color #3 #ffcc66 transparency 0

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

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> color #1 #55ff00 transparency 0

> color #1 springgreen transparency 0

> color #1 lime transparency 0

> color #1 #55ffff transparency 0

> color #1 cyan transparency 0

> color #1 #55ffff transparency 0

> color #1 cyan transparency 0

> hide #!3 models

> open "D:/PhD/Nannochloropsis_oceanica/other algae/6LY5/6ly5.pdb"

6ly5.pdb title:  
Organization and energy transfer In A huge diatom ψ-FCPI supercomplex [more
info...]  
  
Chain information for 6ly5.pdb #5  
---  
Chain | Description  
A | FCPI-7  
B | FCPI-1  
C | FCPI-11  
D | FCPI-6  
E | FCPI-5  
F | FCPI-8  
G | FCPI-4  
H | FCPI-10  
I | FCPI-3  
J | FCPI-9  
K | FCPI-13  
L | FCPI-14  
M | FCPI-16  
N | FCPI-21  
O P Q | FCPI  
R | FCPI-24  
S | FCPI-23  
T | FCPI-12  
U | FCPI-2  
V | FCPI-19  
W | FCPI-17  
X | FCPI-17  
a | PSAA  
b | PSAB  
c | PSAC  
d | PSAD  
e | PSAE  
f | PSAF  
g | PSAS  
h | PSAR  
i | PSAI  
j | PSAJ  
l | PSAL  
m | PSAM  
  
Non-standard residues in 6ly5.pdb #5  
---  
A86 —
(3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-β,β-caroten-3'-
yl acetate (fucoxanthin)  
BCR — β-carotene  
CLA — chlorophyll A  
DD6 —
(3S,3'R,5R,6S,7CIS)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-β,β-carotene-3,3'-diol
(diadinoxanthin)  
DGD — digalactosyl diacyl glycerol (DGDG)  
KC1 — chlorophyll C1  
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole  
LMG — 1,2-distearoyl-monogalactosyl-diglyceride  
LMT — dodecyl-β-D-maltoside  
PQN — phylloquinone (vitamin K1; 2-methyl-3-phytyl-1,4-naphthoquinone)  
SF4 — iron/sulfur cluster  
SQD — 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-α-D-glucopyranosyl]-Sn-glycerol
(sulfoquinovosyldiacylglycerol)  
  

> hide #!1,5 atoms

> show #!1,5 cartoons

> cartoon style #1,5 modeHelix tube sides 20

> color #5 #fa9371 transparency 0

> color #5 #fa856e transparency 0

> ui tool show Matchmaker

> matchmaker #!5 to #1

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 NO0828.pdb, chain A (#1) with 6ly5.pdb, chain a (#5), sequence
alignment score = 3510.8  
RMSD between 737 pruned atom pairs is 0.335 angstroms; (across all 739 pairs:
0.532)  
  

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

> show #!3 models

> hide #!3 models

> hide #!5 models

> open "D:/PhD/Nannochloropsis_oceanica/other algae/7y7b cryptophyte.pdb"

7y7b cryptophyte.pdb title:  
Cryo-em structure of cryptophyte photosystem I [more info...]  
  
Chain information for 7y7b cryptophyte.pdb #6  
---  
Chain | Description  
1 | ACPI-1  
2 | ACPI-2  
3 | ACPI-3  
4 | ACPI-4  
5 | ACPI-5  
6 | ACPI-6  
7 | ACPI-7  
8 | ACPI-8  
9 | ACPI-12  
A | PSAA  
B | PSAB  
C | photosystem I iron-sulfur center  
D | photosystem I reaction center subunit II  
E | photosystem I reaction center subunit IV  
F | PSI-F  
I | photosystem I reaction center subunit VIII  
J | photosystem I reaction center subunit IX  
K | photosystem I subunit X  
L | photosystem I reaction center subunit XI  
M | PSI-M  
O | PSAO  
R | PSAR  
X | UNK1  
Z | ACPI-S  
a d | ACPI-13/10  
b | ACPI-14  
c | ACPI-9  
e | ACPI-11  
  
Non-standard residues in 7y7b cryptophyte.pdb #6  
---  
8CT —
(6'R,11CIS,11'cis,13CIS,15CIS)-4',5'-didehydro-5',6'-dihydro-β,β-carotene  
CLA — chlorophyll A  
DGD — digalactosyl diacyl glycerol (DGDG)  
IHT —
(1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol
(allobetaxanthin)  
II0 —
(1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-
cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol
(alloxanthin)  
II3 —
(1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-
cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol
(monadoxanthin)  
KC2 — chlorophyll C2  
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole  
LMG — 1,2-distearoyl-monogalactosyl-diglyceride  
LMU — dodecyl-α-D-maltoside  
PQN — phylloquinone (vitamin K1; 2-methyl-3-phytyl-1,4-naphthoquinone)  
SF4 — iron/sulfur cluster  
SQD — 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-α-D-glucopyranosyl]-Sn-glycerol
(sulfoquinovosyldiacylglycerol)  
  

> hide #!1,6 atoms

> show #!1,6 cartoons

> cartoon style #1,6 modeHelix tube sides 20

> color #6 #aaaaff transparency 0

> ui tool show Matchmaker

> matchmaker #!6 to #1

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 NO0828.pdb, chain A (#1) with 7y7b cryptophyte.pdb, chain A (#6),
sequence alignment score = 3451.6  
RMSD between 736 pruned atom pairs is 0.586 angstroms; (across all 739 pairs:
0.730)  
  

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

> hide #!6 models

> open "D:/PhD/Nannochloropsis_oceanica/other algae/5zgbCm.pdb"
> "D:/PhD/Nannochloropsis_oceanica/other algae/8jw0Ac.pdb"

5zgbCm.pdb title:  
Cryo-em structure of the red algal ψ-LHCR [more info...]  
  
Chain information for 5zgbCm.pdb #7  
---  
Chain | Description | UniProt  
1 | LHCR1 | M1VKK5_CYAM1  
2 5 | LHCR2 | M1UU36_CYAM1  
3 | LHCR3 |  
4 | LHCR1 | M1VKK5_CYAM1  
A | PSAA | PSAA_CYAM1  
B | PSAB | PSAB_CYAM1  
C | PSAC | PSAC_CYAM1  
D | PSAD | Q85FY0_CYAM1  
E | PSAE | Q85FZ1_CYAM1  
F | PSAF | Q85FS9_CYAM1  
I | PSAI | Q85FQ6_CYAM1  
J | PSI-J | PSAJ_CYAM1  
K | PSAK | Q85G51_CYAM1  
L | PSAL | PSAL_CYAM1  
M | PSI-M | Q85G73_CYAM1  
O | PSAO | M1VFJ4_CYAM1  
  
Non-standard residues in 5zgbCm.pdb #7  
---  
1DO — 1-dodecanol  
3XQ — (2S)-2,3-dihydroxypropyl octadecanoate  
BCR — β-carotene  
BGC — β-D-glucopyranose  
CL0 — chlorophyll A isomer  
CLA — chlorophyll A  
DGD — digalactosyl diacyl glycerol (DGDG)  
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole  
PQN — phylloquinone (vitamin K1; 2-methyl-3-phytyl-1,4-naphthoquinone)  
SF4 — iron/sulfur cluster  
ZEX —
(1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol  
  
8jw0Ac.pdb title:  
Psi-acppci supercomplex from amphidinium carterae [more info...]  
  
Chain information for 8jw0Ac.pdb #8  
---  
Chain | Description  
A | chlorophyll A-chlorophyll C-peridinin-protein-complex I-10, acppci-10  
B | chlorophyll A-chlorophyll C-peridinin-protein-complex I-11, acppci-11  
C | chlorophyll A-chlorophyll C-peridinin-protein-complex I-16, acppci-16  
D | chlorophyll A-chlorophyll C-peridinin-protein-complex I-9, acppci-9  
E | chlorophyll A-chlorophyll C-peridinin-protein-complex I-1, acppci-1  
F | chlorophyll A-chlorophyll C-peridinin-protein-complex I-2, acppci-2  
G | chlorophyll A-chlorophyll C-peridinin-protein-complex I-8, acppci-8  
H | chlorophyll A-chlorophyll C-peridinin-protein-complex I-12, acppci-12  
I | chlorophyll A-chlorophyll C-peridinin-protein-complex I-7, acppci-7  
J | chlorophyll A-chlorophyll C-peridinin-protein-complex I-3, acppci-3  
K | chlorophyll A-chlorophyll C-peridinin-protein-complex I-6, acppci-6  
L | chlorophyll A-chlorophyll C-peridinin-protein-complex I-5, acppci-5  
M | chlorophyll A-chlorophyll C-peridinin-protein-complex I-4, acppci-4  
N | chlorophyll A-chlorophyll C-peridinin-protein-complex I-13, acppci-13  
O | chlorophyll A-chlorophyll C-peridinin-protein-complex I-15, acppci-15  
P | chlorophyll A-chlorophyll C-peridinin-protein-complex I-14, acppci-14  
Q | chlorophyll A-chlorophyll C-peridinin-protein-complex I-17, acppci-17  
T | chlorophyll A-chlorophyll C-peridinin-protein-complex I-16, acppci-16  
a | photosystem I psaa  
b | photosystem I psab  
c | photosystem I psac  
d | photosystem I psad  
e | photosystem I psae  
f | photosystem I psaf  
h | photosystem I psar  
i | photosystem I psai  
j | photosystem I psaj  
l | photosystem I psal  
m | photosystem I psam  
  
Non-standard residues in 8jw0Ac.pdb #8  
---  
BCR — β-carotene  
CLA — chlorophyll A  
DD6 —
(3S,3'R,5R,6S,7CIS)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-β,β-carotene-3,3'-diol
(diadinoxanthin)  
DGD — digalactosyl diacyl glycerol (DGDG)  
KC1 — chlorophyll C1  
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole  
LMG — 1,2-distearoyl-monogalactosyl-diglyceride  
PID — peridinin  
PQN — phylloquinone (vitamin K1; 2-methyl-3-phytyl-1,4-naphthoquinone)  
SF4 — iron/sulfur cluster  
SQD — 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-α-D-glucopyranosyl]-Sn-glycerol
(sulfoquinovosyldiacylglycerol)  
UIX —
[(1~{S},5~{R})-3,3,5-trimethyl-5-oxidanyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenylidene]cyclohexyl]
ethanoate (dinoxanthin)  
  

> hide #!8 models

> ui tool show Matchmaker

> matchmaker #!7-8 to #1

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 NO0828.pdb, chain A (#1) with 5zgbCm.pdb, chain A (#7), sequence
alignment score = 3312.4  
RMSD between 733 pruned atom pairs is 0.858 angstroms; (across all 739 pairs:
0.968)  
  
Matchmaker NO0828.pdb, chain A (#1) with 8jw0Ac.pdb, chain a (#8), sequence
alignment score = 1992.3  
RMSD between 518 pruned atom pairs is 0.897 angstroms; (across all 641 pairs:
4.765)  
  

> show #!8 models

> cartoon style #1,7-8 modeHelix tube sides 20

> hide #!1,7-8 atoms

> show #!1,7-8 cartoons

> color #7 #ff40bc transparency 0

> color #7 #ff31b7 transparency 0

> color #8 #55ff7f transparency 0

> hide #!8 models

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

> hide #!7 models

> show #!8 models

> save C:\Users\qiuyu\Desktop\image3.png supersample 3

> show #!7 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!3 models

> show #!8 models

> hide #!8 models

> hide #!3 models

> show #!8 models

> hide #!7 models

> show #!3 models

> hide #!3 models

> open D:/PhD/Nannochloropsis_oceanica/coot/NO0829.pdb

Chain information for NO0829.pdb #9  
---  
Chain | Description  
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  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
I | No description available  
J | No description available  
L | No description available  
M | No description available  
R | No description available  
X | No description available  
  

> hide #!8 models

> hide #!1 models

> hide #!9 cartoons

> show #!9 cartoons

> hide #!9 atoms

> hide #!9 models

> show #!9 models

> show #!3 models

> save D:/PhD/Nannochloropsis_oceanica/session/NOred.cxs

> save "D:/PhD/Nannochloropsis_oceanica/other algae/8jzeSs_fitNO.pdb" models
> #3 relModel #1

> save "D:/PhD/Nannochloropsis_oceanica/other algae/6LY5fitNO.pdb" models #5
> relModel #1

> save "D:/PhD/Nannochloropsis_oceanica/other
> algae/7y7b_cryptophyte_fitNO.pdb" models #6 relModel #1

> save "D:/PhD/Nannochloropsis_oceanica/other algae/5zgbCm_fitNO.pdb" models
> #7 relModel #1

> save "D:/PhD/Nannochloropsis_oceanica/other algae/8jw0Ac_fitNO.pdb" models
> #8 relModel #1

> close #3

> close #5


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 546.24
OpenGL renderer: NVIDIA GeForce RTX 4060 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUSTeK COMPUTER INC.
Model: ROG Strix G614JV_G614JV
OS: Microsoft Windows 11 家庭中文版 (Build 22631)
Memory: 16,779,960,320
MaxProcessMemory: 137,438,953,344
CPU: 32 13th Gen Intel(R) Core(TM) i9-13980HX
OSLanguage: zh-CN
Locale: ('zh_CN', 'cp936')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    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: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    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: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    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: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 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: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 15 months ago

Component:	Unassigned → Core
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Crash in event loop

comment:2 by Eric Pettersen, 15 months ago

Resolution:	→ can't reproduce
Status:	accepted → closed

Hi Moon,

Thanks for reporting this problem. It's not really clear from the information in the report what precisely caused the crash. Nonetheless I would recommend upgrading to ChimeraX 1.8. Not only have many bugs been fixed relative to your 1.3 version, but 1.8 includes more thorough automatic bug reporting, so that even if this problem has been fix, the report will give us a better chance of diagnosing and fixing it.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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