id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7591 Crash in movie encode (fork ffmpeg) t.sixma@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC) Description Last time you used ChimeraX it crashed. 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All rights reserved. How to cite UCSF ChimeraX > open > /Users/home/surfdrive/Documents_surfdrive/Talks_surfdrive/chains2022/movie- > work/movies-andrea/uchl5/UCHL5_full-range.cxc > delete all > ~hbonds > ~distance > select clear > stop > view orient > open 3a7s.pdb name uchl5-3a7s uchl5-3a7s title: Catalytic domain of UCH37 [more info...] Chain information for uchl5-3a7s #1 --- Chain | Description | UniProt A | ubiquitin carboxyl-terminal hydrolase isozyme L5 | UCHL5_HUMAN Non-standard residues in uchl5-3a7s #1 --- CL — chloride ion > open 3rii-a.pdb name uchl5-3rii Chain information for uchl5-3rii #2 --- Chain | Description A | No description available > open 3ris-a.pdb name uchl5-3ris Chain information for uchl5-3ris #3 --- Chain | Description A | No description available > open 3tb3-a.pdb name uchl5-3tb3 Chain information for uchl5-3tb3 #4 --- Chain | Description A | No description available > open 3ihr.pdb name uchl5-3ihr uchl5-3ihr title: Crystal structure of UCH37 [more info...] Chain information for uchl5-3ihr #5 --- Chain | Description | UniProt A | ubiquitin carboxyl-terminal hydrolase isozyme L5 | UCHL5_HUMAN Non-standard residues in uchl5-3ihr #5 --- FMT — formic acid NA — sodium ion > open l5-4uem.pdb name apoL5_4uem Chain information for apoL5_4uem #6 --- Chain | Description A | No description available > open l5-4uel.pdb name activeL5_4uel Chain information for activeL5_4uel #7 --- Chain | Description A | No description available > open l5-4uf5.pdb name inactivel5_4uf5 Chain information for inactivel5_4uf5 #8 --- Chain | Description A | No description available > open rpn13-4uem.pdb name rpn13-4uem Chain information for rpn13-4uem #9 --- Chain | Description B | No description available > open rpn13-4uel.pdb name rpn13-ub-4uel Chain information for rpn13-ub-4uel #10 --- Chain | Description C | No description available > open ino80-4uf5.pdb name ino80-4uf5 Chain information for ino80-4uf5 #11 --- Chain | Description B | No description available > open ub-4uel.pdb name ub-4uel Chain information for ub-4uel #12 --- Chain | Description B | No description available > open 4UEM.cif 4UEM.cif title: UCH-L5 in complex with the RPN13 DEUBAD domain [more info...] Chain information for 4UEM.cif #13 --- Chain | Description | UniProt A | ubiquitin carboxyl-terminal hydrolase isozyme L5 | UCHL5_HUMAN B | proteasomal ubiquitin receptor ADRM1 | ADRM1_HUMAN > open 4UEL.cif 4UEL.cif title: UCH-L5 in complex with ubiquitin-propargyl bound to the RPN13 DEUBAD domain [more info...] Chain information for 4UEL.cif #14 --- Chain | Description | UniProt A | ubiquitin carboxyl-terminal hydrolase isozyme L5 | UCHL5_HUMAN B | polyubiquitin-B | UBB_HUMAN C | proteasomal ubiquitin receptor ADRM1 | ADRM1_HUMAN Non-standard residues in 4UEL.cif #14 --- AYE — prop-2-en-1-amine (allylamine) > open 4UF5.cif 4UF5.cif title: Crystal structure of UCH-L5 in complex with inhibitory fragment of INO80G [more info...] Chain information for 4UF5.cif #15 --- Chain | Description | UniProt A | ubiquitin carboxyl-terminal hydrolase isozyme L5 | UCHL5_HUMAN B | nuclear factor related to κ-B-binding protein | NFRKB_HUMAN > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs 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 nucleotides tube/slab shape box > set bgColor white > graphics silhouettes false > lighting simple > name L5-1 #1/A > name L5-2 #2/A > name L5-3 #3/A > name L5-4 #4/A > name L5-5 #5/A > name L5-apo #6 > name L5-active #7 > name L5-inactive #8 > name rpn13-apo #9 > name rpn13-active #10 > name ub #10 > name Uld #1-12/A:225-350 > name ULD-rpn13 #9/A:225-350 > name ULD-ino80 #11/A:225-350 > matchmaker #2-8/A to #1/A 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 uchl5-3a7s, chain A (#1) with uchl5-3rii, chain A (#2), sequence alignment score = 981.8 RMSD between 199 pruned atom pairs is 0.515 angstroms; (across all 204 pairs: 0.699) Matchmaker uchl5-3a7s, chain A (#1) with uchl5-3ris, chain A (#3), sequence alignment score = 982.5 RMSD between 201 pruned atom pairs is 0.652 angstroms; (across all 204 pairs: 0.740) Matchmaker uchl5-3a7s, chain A (#1) with uchl5-3tb3, chain A (#4), sequence alignment score = 1009.7 RMSD between 200 pruned atom pairs is 0.621 angstroms; (across all 204 pairs: 0.805) Matchmaker uchl5-3a7s, chain A (#1) with uchl5-3ihr, chain A (#5), sequence alignment score = 1006 RMSD between 190 pruned atom pairs is 0.687 angstroms; (across all 203 pairs: 0.998) Matchmaker uchl5-3a7s, chain A (#1) with apoL5_4uem, chain A (#6), sequence alignment score = 935.5 RMSD between 179 pruned atom pairs is 0.801 angstroms; (across all 198 pairs: 2.497) Matchmaker uchl5-3a7s, chain A (#1) with activeL5_4uel, chain A (#7), sequence alignment score = 954.3 RMSD between 176 pruned atom pairs is 0.874 angstroms; (across all 204 pairs: 1.541) Matchmaker uchl5-3a7s, chain A (#1) with inactivel5_4uf5, chain A (#8), sequence alignment score = 984.9 RMSD between 191 pruned atom pairs is 0.822 angstroms; (across all 204 pairs: 1.111) > matchmaker #13-15/A to #1/A 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 uchl5-3a7s, chain A (#1) with 4UEM.cif, chain A (#13), sequence alignment score = 963.3 RMSD between 179 pruned atom pairs is 0.801 angstroms; (across all 196 pairs: 1.209) Matchmaker uchl5-3a7s, chain A (#1) with 4UEL.cif, chain A (#14), sequence alignment score = 948.3 RMSD between 176 pruned atom pairs is 0.874 angstroms; (across all 204 pairs: 1.541) Matchmaker uchl5-3a7s, chain A (#1) with 4UF5.cif, chain A (#15), sequence alignment score = 972.9 RMSD between 191 pruned atom pairs is 0.822 angstroms; (across all 204 pairs: 1.111) > matchmaker #9/B to #13/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 4UEM.cif, chain B (#13) with rpn13-4uem, chain B (#9), sequence alignment score = 499.5 RMSD between 98 pruned atom pairs is 0.000 angstroms; (across all 98 pairs: 0.000) > matchmaker #10/C to #14/C 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 4UEL.cif, chain C (#14) with rpn13-ub-4uel, chain C (#10), sequence alignment score = 498.9 RMSD between 98 pruned atom pairs is 0.000 angstroms; (across all 98 pairs: 0.000) > matchmaker #11/B to #15/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 4UF5.cif, chain B (#15) with ino80-4uf5, chain B (#11), sequence alignment score = 582.8 RMSD between 110 pruned atom pairs is 0.000 angstroms; (across all 110 pairs: 0.000) > matchmaker #12/B to #14/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 4UEL.cif, chain B (#14) with ub-4uel, chain B (#12), sequence alignment score = 376.5 RMSD between 75 pruned atom pairs is 0.000 angstroms; (across all 75 pairs: 0.000) > view > view matrix camera > 0.73046,0.077942,-0.67851,-121.86,0.43998,-0.81354,0.38022,86.379,-0.52235,-0.57627,-0.62854,-136.47 > view name view2 > view matrix camera > 0.32874,0.87188,0.363,114.86,0.061267,-0.40325,0.91304,222.83,0.94243,-0.27791,-0.186,-31.174 > view name overview1 > view overview1 > colordef rpn13 lawn green Color 'rpn13' is opaque: rgb(48.6%, 98.8%, 0%) hex: #7cfc00 > colordef ino80 orange red Color 'ino80' is opaque: rgb(100%, 27.1%, 0%) hex: #ff4500 > colordef generic #e6e7e8 Color 'generic' is opaque: rgb(90.2%, 90.6%, 91%) hex: #e6e7e8 > colordef ub gold Color 'ub' is opaque: rgb(100%, 84.3%, 0%) hex: #ffd700 > colordef l5active silver Color 'l5active' is opaque: gray(75.3%) hex: #c0c0c0 > colordef l5inactive silver Color 'l5inactive' is opaque: gray(75.3%) hex: #c0c0c0 > colordef uld light steel blue Color 'uld' is opaque: rgb(69%, 76.9%, 87.1%) hex: #b0c4de > colordef l5 royal blue Color 'l5' is opaque: rgb(25.5%, 41.2%, 88.2%) hex: #4169e1 > color #12 ub > color #1-8 l5 > color all byhetero > color Uld uld > color #9 rpn13 > color #11 ino80 > cofr 20.394, -3.2716, 33.906 > hide all > hide cartoons > movie record > show #7 cartoons > rock x 30 cycle 120 > rock y 30 cycle 120 > wait 60 > show #12 cartoons > wait 60 > show #9 cartoons > wait 120 > hide #9,12 cartoons > morph #7,8 hideModels false frames 60 Computed 61 frame morph #16 > coordset #16 1,61 > color #16 uld > hide cartoons > stop > cofr 39.217, 12.068, 15.496 > matchmaker #15/A:225-350 to #13/A:225-350 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 4UEM.cif, chain A (#13) with 4UF5.cif, chain A (#15), sequence alignment score = 396.4 RMSD between 33 pruned atom pairs is 1.272 angstroms; (across all 81 pairs: 4.378) > name ULD-ino80 #15/A:225-350 > name ULD-rpn13 #13/A:225-350 > name moved-ino80 #15/B > name new-rpn13 #13/B > color moved-ino80 orange red > color new-rpn13 lawn green > color ULD-rpn13 uld > color ULD-ino80 uld > cofr 39.217, 12.068, 15.496 > show ULD-rpn13 cartoons > wait 20 > rock X 30 cycle 120 > show new-rpn13 cartoons > wait 30 > show ULD-ino80 cartoons > show moved-ino80 cartoons > wait 120 > hide moved-ino80 cartoons > hide new-rpn13 cartoons > hide ULD-ino80 cartoons > wait 30 > show #16 cartoons > coordset #16 1,60 bounce true loop 2 > coordset #16 1,60 > show #7,8 models > show #7 cartoons > show #8 cartoons > wait 180 > hide #7,16 cartoons > show #11 cartoons > wait 120 > show #12 cartoons > wait 120 > hide #12 cartoons > wait 120 > movie stop > movie encode uchl5-test.mp4 Movie saved to uchl5-test.mp4 executed UCHL5_full-range.cxc > stop > open > /Users/home/surfdrive/Documents_surfdrive/Talks_surfdrive/chains2022/movie- > work/movies-andrea/uchl5/UCHL5_full-range.cxc > delete all > ~hbonds > ~distance > select clear > stop > view orient > open 3a7s.pdb name uchl5-3a7s uchl5-3a7s title: Catalytic domain of UCH37 [more info...] Chain information for uchl5-3a7s #1 --- Chain | Description | UniProt A | ubiquitin carboxyl-terminal hydrolase isozyme L5 | UCHL5_HUMAN Non-standard residues in uchl5-3a7s #1 --- CL — chloride ion > open 3rii-a.pdb name uchl5-3rii Chain information for uchl5-3rii #2 --- Chain | Description A | No description available > open 3ris-a.pdb name uchl5-3ris Chain information for uchl5-3ris #3 --- Chain | Description A | No description available > open 3tb3-a.pdb name uchl5-3tb3 Chain information for uchl5-3tb3 #4 --- Chain | Description A | No description available > open 3ihr.pdb name uchl5-3ihr uchl5-3ihr title: Crystal structure of UCH37 [more info...] Chain information for uchl5-3ihr #5 --- Chain | Description | UniProt A | ubiquitin carboxyl-terminal hydrolase isozyme L5 | UCHL5_HUMAN Non-standard residues in uchl5-3ihr #5 --- FMT — formic acid NA — sodium ion > open l5-4uem.pdb name apoL5_4uem Chain information for apoL5_4uem #6 --- Chain | Description A | No description available > open l5-4uel.pdb name activeL5_4uel Chain information for activeL5_4uel #7 --- Chain | Description A | No description available > open l5-4uf5.pdb name inactivel5_4uf5 Chain information for inactivel5_4uf5 #8 --- Chain | Description A | No description available > open rpn13-4uem.pdb name rpn13-4uem Chain information for rpn13-4uem #9 --- Chain | Description B | No description available > open rpn13-4uel.pdb name rpn13-ub-4uel Chain information for rpn13-ub-4uel #10 --- Chain | Description C | No description available > open ino80-4uf5.pdb name ino80-4uf5 Chain information for ino80-4uf5 #11 --- Chain | Description B | No description available > open ub-4uel.pdb name ub-4uel Chain information for ub-4uel #12 --- Chain | Description B | No description available > open 4UEM.cif 4UEM.cif title: UCH-L5 in complex with the RPN13 DEUBAD domain [more info...] Chain information for 4UEM.cif #13 --- Chain | Description | UniProt A | ubiquitin carboxyl-terminal hydrolase isozyme L5 | UCHL5_HUMAN B | proteasomal ubiquitin receptor ADRM1 | ADRM1_HUMAN > open 4UEL.cif 4UEL.cif title: UCH-L5 in complex with ubiquitin-propargyl bound to the RPN13 DEUBAD domain [more info...] Chain information for 4UEL.cif #14 --- Chain | Description | UniProt A | ubiquitin carboxyl-terminal hydrolase isozyme L5 | UCHL5_HUMAN B | polyubiquitin-B | UBB_HUMAN C | proteasomal ubiquitin receptor ADRM1 | ADRM1_HUMAN Non-standard residues in 4UEL.cif #14 --- AYE — prop-2-en-1-amine (allylamine) > open 4UF5.cif 4UF5.cif title: Crystal structure of UCH-L5 in complex with inhibitory fragment of INO80G [more info...] Chain information for 4UF5.cif #15 --- Chain | Description | UniProt A | ubiquitin carboxyl-terminal hydrolase isozyme L5 | UCHL5_HUMAN B | nuclear factor related to κ-B-binding protein | NFRKB_HUMAN > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs 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 nucleotides tube/slab shape box > set bgColor white > graphics silhouettes false > lighting simple > name L5-1 #1/A > name L5-2 #2/A > name L5-3 #3/A > name L5-4 #4/A > name L5-5 #5/A > name L5-apo #6 > name L5-active #7 > name L5-inactive #8 > name rpn13-apo #9 > name rpn13-active #10 > name ub #10 > name Uld #1-12/A:225-350 > name ULD-rpn13 #9/A:225-350 > name ULD-ino80 #11/A:225-350 > matchmaker #2-8/A to #1/A 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 uchl5-3a7s, chain A (#1) with uchl5-3rii, chain A (#2), sequence alignment score = 981.8 RMSD between 199 pruned atom pairs is 0.515 angstroms; (across all 204 pairs: 0.699) Matchmaker uchl5-3a7s, chain A (#1) with uchl5-3ris, chain A (#3), sequence alignment score = 982.5 RMSD between 201 pruned atom pairs is 0.652 angstroms; (across all 204 pairs: 0.740) Matchmaker uchl5-3a7s, chain A (#1) with uchl5-3tb3, chain A (#4), sequence alignment score = 1009.7 RMSD between 200 pruned atom pairs is 0.621 angstroms; (across all 204 pairs: 0.805) Matchmaker uchl5-3a7s, chain A (#1) with uchl5-3ihr, chain A (#5), sequence alignment score = 1006 RMSD between 190 pruned atom pairs is 0.687 angstroms; (across all 203 pairs: 0.998) Matchmaker uchl5-3a7s, chain A (#1) with apoL5_4uem, chain A (#6), sequence alignment score = 935.5 RMSD between 179 pruned atom pairs is 0.801 angstroms; (across all 198 pairs: 2.497) Matchmaker uchl5-3a7s, chain A (#1) with activeL5_4uel, chain A (#7), sequence alignment score = 954.3 RMSD between 176 pruned atom pairs is 0.874 angstroms; (across all 204 pairs: 1.541) Matchmaker uchl5-3a7s, chain A (#1) with inactivel5_4uf5, chain A (#8), sequence alignment score = 984.9 RMSD between 191 pruned atom pairs is 0.822 angstroms; (across all 204 pairs: 1.111) > matchmaker #13-15/A to #1/A 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 uchl5-3a7s, chain A (#1) with 4UEM.cif, chain A (#13), sequence alignment score = 963.3 RMSD between 179 pruned atom pairs is 0.801 angstroms; (across all 196 pairs: 1.209) Matchmaker uchl5-3a7s, chain A (#1) with 4UEL.cif, chain A (#14), sequence alignment score = 948.3 RMSD between 176 pruned atom pairs is 0.874 angstroms; (across all 204 pairs: 1.541) Matchmaker uchl5-3a7s, chain A (#1) with 4UF5.cif, chain A (#15), sequence alignment score = 972.9 RMSD between 191 pruned atom pairs is 0.822 angstroms; (across all 204 pairs: 1.111) > matchmaker #9/B to #13/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 4UEM.cif, chain B (#13) with rpn13-4uem, chain B (#9), sequence alignment score = 499.5 RMSD between 98 pruned atom pairs is 0.000 angstroms; (across all 98 pairs: 0.000) > matchmaker #10/C to #14/C 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 4UEL.cif, chain C (#14) with rpn13-ub-4uel, chain C (#10), sequence alignment score = 498.9 RMSD between 98 pruned atom pairs is 0.000 angstroms; (across all 98 pairs: 0.000) > matchmaker #11/B to #15/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 4UF5.cif, chain B (#15) with ino80-4uf5, chain B (#11), sequence alignment score = 582.8 RMSD between 110 pruned atom pairs is 0.000 angstroms; (across all 110 pairs: 0.000) > matchmaker #12/B to #14/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 4UEL.cif, chain B (#14) with ub-4uel, chain B (#12), sequence alignment score = 376.5 RMSD between 75 pruned atom pairs is 0.000 angstroms; (across all 75 pairs: 0.000) > view > view matrix camera > 0.73046,0.077942,-0.67851,-121.86,0.43998,-0.81354,0.38022,86.379,-0.52235,-0.57627,-0.62854,-136.47 > view name view2 > view matrix camera > 0.32874,0.87188,0.363,114.86,0.061267,-0.40325,0.91304,222.83,0.94243,-0.27791,-0.186,-31.174 > view name overview1 > view overview1 > colordef rpn13 lawn green Color 'rpn13' is opaque: rgb(48.6%, 98.8%, 0%) hex: #7cfc00 > colordef ino80 orange red Color 'ino80' is opaque: rgb(100%, 27.1%, 0%) hex: #ff4500 > colordef generic #e6e7e8 Color 'generic' is opaque: rgb(90.2%, 90.6%, 91%) hex: #e6e7e8 > colordef ub gold Color 'ub' is opaque: rgb(100%, 84.3%, 0%) hex: #ffd700 > colordef l5active silver Color 'l5active' is opaque: gray(75.3%) hex: #c0c0c0 > colordef l5inactive silver Color 'l5inactive' is opaque: gray(75.3%) hex: #c0c0c0 > colordef uld light steel blue Color 'uld' is opaque: rgb(69%, 76.9%, 87.1%) hex: #b0c4de > colordef l5 royal blue Color 'l5' is opaque: rgb(25.5%, 41.2%, 88.2%) hex: #4169e1 > color #12 ub > color #1-8 l5 > color all byhetero > color Uld uld > color #9 rpn13 > color #11 ino80 > cofr 20.394, -3.2716, 33.906 > hide all > hide cartoons > movie record > show #7 cartoons > rock x 30 cycle 120 > rock y 30 cycle 120 > wait 60 > show #12 cartoons > wait 60 > show #9 cartoons > wait 120 > hide #9,12 cartoons > morph #7,8 hideModels false frames 60 Computed 61 frame morph #16 > coordset #16 1,61 > color #16 uld > hide cartoons > stop > cofr 39.217, 12.068, 15.496 > matchmaker #15/A:225-350 to #13/A:225-350 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 4UEM.cif, chain A (#13) with 4UF5.cif, chain A (#15), sequence alignment score = 396.4 RMSD between 33 pruned atom pairs is 1.272 angstroms; (across all 81 pairs: 4.378) > name ULD-ino80 #15/A:225-350 > name ULD-rpn13 #13/A:225-350 > name moved-ino80 #15/B > name new-rpn13 #13/B > color moved-ino80 orange red > color new-rpn13 lawn green > color ULD-rpn13 uld > color ULD-ino80 uld > cofr 39.217, 12.068, 15.496 > show ULD-rpn13 cartoons > wait 20 > rock X 30 cycle 120 > show new-rpn13 cartoons > wait 30 > show ULD-ino80 cartoons > show moved-ino80 cartoons > wait 120 > hide moved-ino80 cartoons > hide new-rpn13 cartoons > hide ULD-ino80 cartoons > wait 30 > show #16 cartoons > coordset #16 1,60 bounce true loop 2 > show #7,8 models > show #7 cartoons > show #8 cartoons > wait 90 > show #9 cartoons > wait 30 > hide #9 cartoons > coordset #16 1,60 > hide #7,16 cartoons > show #11 cartoons > wait 120 > show #12 cartoons > wait 120 > hide #12 cartoons > wait 120 > movie stop > movie encode uchl5-test.mp4 Movie saved to uchl5-test.mp4 executed UCHL5_full-range.cxc > stop > open > /Users/home/surfdrive/Documents_surfdrive/Talks_surfdrive/chains2022/movie- > work/movies-andrea/uchl5/UCHL5_full-range.cxc > delete all > ~hbonds > ~distance > select clear > stop > view orient > open 3a7s.pdb name uchl5-3a7s uchl5-3a7s title: Catalytic domain of UCH37 [more info...] Chain information for uchl5-3a7s #1 --- Chain | Description | UniProt A | ubiquitin carboxyl-terminal hydrolase isozyme L5 | UCHL5_HUMAN Non-standard residues in uchl5-3a7s #1 --- CL — chloride ion > open 3rii-a.pdb name uchl5-3rii Chain information for uchl5-3rii #2 --- Chain | Description A | No description available > open 3ris-a.pdb name uchl5-3ris Chain information for uchl5-3ris #3 --- Chain | Description A | No description available > open 3tb3-a.pdb name uchl5-3tb3 Chain information for uchl5-3tb3 #4 --- Chain | Description A | No description available > open 3ihr.pdb name uchl5-3ihr uchl5-3ihr title: Crystal structure of UCH37 [more info...] Chain information for uchl5-3ihr #5 --- Chain | Description | UniProt A | ubiquitin carboxyl-terminal hydrolase isozyme L5 | UCHL5_HUMAN Non-standard residues in uchl5-3ihr #5 --- FMT — formic acid NA — sodium ion > open l5-4uem.pdb name apoL5_4uem Chain information for apoL5_4uem #6 --- Chain | Description A | No description available > open l5-4uel.pdb name activeL5_4uel Chain information for activeL5_4uel #7 --- Chain | Description A | No description available > open l5-4uf5.pdb name inactivel5_4uf5 Chain information for inactivel5_4uf5 #8 --- Chain | Description A | No description available > open rpn13-4uem.pdb name rpn13-4uem Chain information for rpn13-4uem #9 --- Chain | Description B | No description available > open rpn13-4uel.pdb name rpn13-ub-4uel Chain information for rpn13-ub-4uel #10 --- Chain | Description C | No description available > open ino80-4uf5.pdb name ino80-4uf5 Chain information for ino80-4uf5 #11 --- Chain | Description B | No description available > open ub-4uel.pdb name ub-4uel Chain information for ub-4uel #12 --- Chain | Description B | No description available > open 4UEM.cif 4UEM.cif title: UCH-L5 in complex with the RPN13 DEUBAD domain [more info...] Chain information for 4UEM.cif #13 --- Chain | Description | UniProt A | ubiquitin carboxyl-terminal hydrolase isozyme L5 | UCHL5_HUMAN B | proteasomal ubiquitin receptor ADRM1 | ADRM1_HUMAN > open 4UEL.cif 4UEL.cif title: UCH-L5 in complex with ubiquitin-propargyl bound to the RPN13 DEUBAD domain [more info...] Chain information for 4UEL.cif #14 --- Chain | Description | UniProt A | ubiquitin carboxyl-terminal hydrolase isozyme L5 | UCHL5_HUMAN B | polyubiquitin-B | UBB_HUMAN C | proteasomal ubiquitin receptor ADRM1 | ADRM1_HUMAN Non-standard residues in 4UEL.cif #14 --- AYE — prop-2-en-1-amine (allylamine) > open 4UF5.cif 4UF5.cif title: Crystal structure of UCH-L5 in complex with inhibitory fragment of INO80G [more info...] Chain information for 4UF5.cif #15 --- Chain | Description | UniProt A | ubiquitin carboxyl-terminal hydrolase isozyme L5 | UCHL5_HUMAN B | nuclear factor related to κ-B-binding protein | NFRKB_HUMAN > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs 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 nucleotides tube/slab shape box > set bgColor white > graphics silhouettes false > lighting simple > name L5-1 #1/A > name L5-2 #2/A > name L5-3 #3/A > name L5-4 #4/A > name L5-5 #5/A > name L5-apo #6 > name L5-active #7 > name L5-inactive #8 > name rpn13-apo #9 > name rpn13-active #10 > name ub #10 > name Uld #1-12/A:225-350 > name ULD-rpn13 #9/A:225-350 > name ULD-ino80 #11/A:225-350 > matchmaker #2-8/A to #1/A 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 uchl5-3a7s, chain A (#1) with uchl5-3rii, chain A (#2), sequence alignment score = 981.8 RMSD between 199 pruned atom pairs is 0.515 angstroms; (across all 204 pairs: 0.699) Matchmaker uchl5-3a7s, chain A (#1) with uchl5-3ris, chain A (#3), sequence alignment score = 982.5 RMSD between 201 pruned atom pairs is 0.652 angstroms; (across all 204 pairs: 0.740) Matchmaker uchl5-3a7s, chain A (#1) with uchl5-3tb3, chain A (#4), sequence alignment score = 1009.7 RMSD between 200 pruned atom pairs is 0.621 angstroms; (across all 204 pairs: 0.805) Matchmaker uchl5-3a7s, chain A (#1) with uchl5-3ihr, chain A (#5), sequence alignment score = 1006 RMSD between 190 pruned atom pairs is 0.687 angstroms; (across all 203 pairs: 0.998) Matchmaker uchl5-3a7s, chain A (#1) with apoL5_4uem, chain A (#6), sequence alignment score = 935.5 RMSD between 179 pruned atom pairs is 0.801 angstroms; (across all 198 pairs: 2.497) Matchmaker uchl5-3a7s, chain A (#1) with activeL5_4uel, chain A (#7), sequence alignment score = 954.3 RMSD between 176 pruned atom pairs is 0.874 angstroms; (across all 204 pairs: 1.541) Matchmaker uchl5-3a7s, chain A (#1) with inactivel5_4uf5, chain A (#8), sequence alignment score = 984.9 RMSD between 191 pruned atom pairs is 0.822 angstroms; (across all 204 pairs: 1.111) > matchmaker #13-15/A to #1/A 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 uchl5-3a7s, chain A (#1) with 4UEM.cif, chain A (#13), sequence alignment score = 963.3 RMSD between 179 pruned atom pairs is 0.801 angstroms; (across all 196 pairs: 1.209) Matchmaker uchl5-3a7s, chain A (#1) with 4UEL.cif, chain A (#14), sequence alignment score = 948.3 RMSD between 176 pruned atom pairs is 0.874 angstroms; (across all 204 pairs: 1.541) Matchmaker uchl5-3a7s, chain A (#1) with 4UF5.cif, chain A (#15), sequence alignment score = 972.9 RMSD between 191 pruned atom pairs is 0.822 angstroms; (across all 204 pairs: 1.111) > matchmaker #9/B to #13/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 4UEM.cif, chain B (#13) with rpn13-4uem, chain B (#9), sequence alignment score = 499.5 RMSD between 98 pruned atom pairs is 0.000 angstroms; (across all 98 pairs: 0.000) > matchmaker #10/C to #14/C 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 4UEL.cif, chain C (#14) with rpn13-ub-4uel, chain C (#10), sequence alignment score = 498.9 RMSD between 98 pruned atom pairs is 0.000 angstroms; (across all 98 pairs: 0.000) > matchmaker #11/B to #15/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 4UF5.cif, chain B (#15) with ino80-4uf5, chain B (#11), sequence alignment score = 582.8 RMSD between 110 pruned atom pairs is 0.000 angstroms; (across all 110 pairs: 0.000) > matchmaker #12/B to #14/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 4UEL.cif, chain B (#14) with ub-4uel, chain B (#12), sequence alignment score = 376.5 RMSD between 75 pruned atom pairs is 0.000 angstroms; (across all 75 pairs: 0.000) > view > view matrix camera > 0.73046,0.077942,-0.67851,-121.86,0.43998,-0.81354,0.38022,86.379,-0.52235,-0.57627,-0.62854,-136.47 > view name view2 > view matrix camera > 0.32874,0.87188,0.363,114.86,0.061267,-0.40325,0.91304,222.83,0.94243,-0.27791,-0.186,-31.174 > view name overview1 > view overview1 > colordef rpn13 lawn green Color 'rpn13' is opaque: rgb(48.6%, 98.8%, 0%) hex: #7cfc00 > colordef ino80 orange red Color 'ino80' is opaque: rgb(100%, 27.1%, 0%) hex: #ff4500 > colordef generic #e6e7e8 Color 'generic' is opaque: rgb(90.2%, 90.6%, 91%) hex: #e6e7e8 > colordef ub gold Color 'ub' is opaque: rgb(100%, 84.3%, 0%) hex: #ffd700 > colordef l5active silver Color 'l5active' is opaque: gray(75.3%) hex: #c0c0c0 > colordef l5inactive silver Color 'l5inactive' is opaque: gray(75.3%) hex: #c0c0c0 > colordef uld light steel blue Color 'uld' is opaque: rgb(69%, 76.9%, 87.1%) hex: #b0c4de > colordef l5 royal blue Color 'l5' is opaque: rgb(25.5%, 41.2%, 88.2%) hex: #4169e1 > color #12 ub > color #1-8 l5 > color all byhetero > color Uld uld > color #9 rpn13 > color #11 ino80 > cofr 20.394, -3.2716, 33.906 > hide all > hide cartoons > movie record > show #7 cartoons > rock x 30 cycle 120 > rock y 30 cycle 120 > wait 60 > show #12 cartoons > wait 60 > show #9 cartoons > wait 120 > hide #9,12 cartoons > morph #7,8 hideModels false frames 60 Computed 61 frame morph #16 > coordset #16 1,61 > color #16 uld > hide cartoons > stop > cofr 39.217, 12.068, 15.496 > matchmaker #15/A:225-350 to #13/A:225-350 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 4UEM.cif, chain A (#13) with 4UF5.cif, chain A (#15), sequence alignment score = 396.4 RMSD between 33 pruned atom pairs is 1.272 angstroms; (across all 81 pairs: 4.378) > name ULD-ino80 #15/A:225-350 > name ULD-rpn13 #13/A:225-350 > name moved-ino80 #15/B > name new-rpn13 #13/B > color moved-ino80 orange red > color new-rpn13 lawn green > color ULD-rpn13 uld > color ULD-ino80 uld > cofr 39.217, 12.068, 15.496 > show ULD-rpn13 cartoons > wait 20 > rock X 30 cycle 120 > show new-rpn13 cartoons > wait 30 > show ULD-ino80 cartoons > show moved-ino80 cartoons > wait 120 > hide moved-ino80 cartoons > hide new-rpn13 cartoons > hide ULD-ino80 cartoons > wait 30 > show #16 cartoons > coordset #16 1,60 bounce true loop 2 > show #7,8 models > show #7 cartoons > show #8 cartoons > wait 120 > show #9 cartoons > wait 30 > hide #9 cartoons > coordset #16 1,60 > hide #7,16 cartoons > wait 60 > show #11 cartoons > wait 90 > show #12 cartoons > wait 60 > hide #12 cartoons > wait 120 > movie stop > movie encode uchl5-test.mp4 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: MacBookAir10,1 Processor Name: Unknown Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache: 8 MB Memory: 8 GB Software: System Software Overview: System Version: macOS 12.4 (21F79) Kernel Version: Darwin 21.5.0 Time since boot: 3 days 17:19 Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.10.8 cftime: 1.6.0 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.4.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.39.1 ChimeraX-AtomicLibrary: 7.0 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.7 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: 2.2.4 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4 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: 1.1 ChimeraX-DistMonitor: 1.1.5 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.2 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: 1.1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 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: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.5 ChimeraX-ModelPanel: 1.3.2 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: 1.9 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 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: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.6 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: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.18.3 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 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: 1.1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.6.0 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.33.3 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.10.0 kiwisolver: 1.4.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.5 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openvr: 1.16.802 packaging: 21.0 ParmEd: 3.4.3 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.29 psutil: 5.9.0 ptyprocess: 0.7.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.0 PyQt6-Qt6: 6.3.0 PyQt6-sip: 13.3.1 PyQt6-WebEngine-commercial: 6.3.0 PyQt6-WebEngine-Qt6: 6.3.0 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 23.1.0 qtconsole: 5.3.0 QtPy: 2.1.0 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 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-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 }}} " defect closed normal Platform limitation Tom Goddard all ChimeraX