id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15848 Crash in event loop 745324914@… Eric Pettersen "{{{ 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 }}} " defect closed normal Core can't reproduce all ChimeraX