id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9990 Error opening zero-length session file in DropBox lp212@… Greg Couch "{{{ The following bug report has been submitted: Platform: macOS-13.5-arm64-arm-64bit ChimeraX Version: 1.5.dev202210110346 (2022-10-11 03:46:09 UTC) Description Open session (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.5.dev202210110346 (2022-10-11) © 2016-2022 Regents of the University of California. All rights reserved. > open ""/Users/lp212/Dropbox (Cambridge University)/GRANTS/ERG Synergy > REPLITARG/research/Predictome structures/AND-1/Psf2.cxs"" Log from Wed Oct 11 12:40:04 2023UCSF ChimeraX version: 1.7.dev202306060017 (2023-06-06) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/luca/Dropbox (Cambridge University)/GRANTS/ERG Synergy > REPLITARG/Predictome structures/AND-1/Psf2.cxs"" Log from Mon Oct 9 16:37:25 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/lp212/Dropbox (Cambridge University)/GRANTS/ERG Synergy > REPLITARG/Predictome structures/AND-1/Psf2.cxs"" Log from Sun Oct 8 20:39:28 2023You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.4.dev202205042108 (2022-05-04) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/lp212/Downloads/DPOLA_HUMAN__WDHD1_HUMAN__2591aa_unrelaxed_af2mv3_model_1.pdb Chain information for DPOLA_HUMAN__WDHD1_HUMAN__2591aa_unrelaxed_af2mv3_model_1.pdb #1 --- Chain | Description A | No description available B | No description available > open > /Users/lp212/Downloads/DPOLA_HUMAN__WDHD1_HUMAN__2591aa_unrelaxed_af2mv3_model_4.pdb Chain information for DPOLA_HUMAN__WDHD1_HUMAN__2591aa_unrelaxed_af2mv3_model_4.pdb #2 --- Chain | Description A | No description available B | No description available > open > /Users/lp212/Downloads/DPOLA_HUMAN__WDHD1_HUMAN__2591aa_unrelaxed_af2mv3_model_2.pdb Chain information for DPOLA_HUMAN__WDHD1_HUMAN__2591aa_unrelaxed_af2mv3_model_2.pdb #3 --- Chain | Description A | No description available B | No description available > ui tool show Matchmaker > matchmaker #2-3 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 DPOLA_HUMAN__WDHD1_HUMAN__2591aa_unrelaxed_af2mv3_model_1.pdb, chain A (#1) with DPOLA_HUMAN__WDHD1_HUMAN__2591aa_unrelaxed_af2mv3_model_4.pdb, chain A (#2), sequence alignment score = 7370.4 RMSD between 976 pruned atom pairs is 0.405 angstroms; (across all 1462 pairs: 23.776) Matchmaker DPOLA_HUMAN__WDHD1_HUMAN__2591aa_unrelaxed_af2mv3_model_1.pdb, chain A (#1) with DPOLA_HUMAN__WDHD1_HUMAN__2591aa_unrelaxed_af2mv3_model_2.pdb, chain A (#3), sequence alignment score = 7415.4 RMSD between 869 pruned atom pairs is 0.264 angstroms; (across all 1462 pairs: 38.394) Drag select of 80 residues > select clear > hide #3 models > hide #2 models > select #2/B 8844 atoms, 9023 bonds, 1129 residues, 1 model selected > select #1/A 11655 atoms, 11889 bonds, 1462 residues, 1 model selected > color sel orange red > select #1/B 8844 atoms, 9023 bonds, 1129 residues, 1 model selected > color sel light sea green > select clear > show #2 models > hide #1 models > show #1 models > hide #1 models > select #2/A 11655 atoms, 11889 bonds, 1462 residues, 1 model selected > color sel orange red > select clear > select #2/B 8844 atoms, 9023 bonds, 1129 residues, 1 model selected > color sel light sea green > select clear > show #1 models > hide #2 models > show #2 models > show #3 models > hide #2 models > hide #1 models > select #3/A 11655 atoms, 11889 bonds, 1462 residues, 1 model selected > color sel orange red > select clear > select #3/B 8844 atoms, 9023 bonds, 1129 residues, 1 model selected > color sel light sea green > select clear > save ""/Users/lp212/Dropbox (Cambridge University)/GRANTS/ERG Synergy > REPLITARG/Predictome structures/AND-1/POLA1.cxs"" > close session > open > /Users/lp212/Downloads/DPOA2_HUMAN__WDHD1_HUMAN__1727aa_unrelaxed_af2mv3_model_1.pdb Chain information for DPOA2_HUMAN__WDHD1_HUMAN__1727aa_unrelaxed_af2mv3_model_1.pdb #1 --- Chain | Description A | No description available B | No description available > open > /Users/lp212/Downloads/DPOA2_HUMAN__WDHD1_HUMAN__1727aa_unrelaxed_af2mv3_model_4.pdb Chain information for DPOA2_HUMAN__WDHD1_HUMAN__1727aa_unrelaxed_af2mv3_model_4.pdb #2 --- Chain | Description A | No description available B | No description available > open > /Users/lp212/Downloads/DPOA2_HUMAN__WDHD1_HUMAN__1727aa_unrelaxed_af2mv3_model_2.pdb Chain information for DPOA2_HUMAN__WDHD1_HUMAN__1727aa_unrelaxed_af2mv3_model_2.pdb #3 --- Chain | Description A | No description available B | No description available > ui tool show Matchmaker > matchmaker #2-3 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 DPOA2_HUMAN__WDHD1_HUMAN__1727aa_unrelaxed_af2mv3_model_1.pdb, chain B (#1) with DPOA2_HUMAN__WDHD1_HUMAN__1727aa_unrelaxed_af2mv3_model_4.pdb, chain B (#2), sequence alignment score = 5730.2 RMSD between 413 pruned atom pairs is 0.467 angstroms; (across all 1129 pairs: 59.540) Matchmaker DPOA2_HUMAN__WDHD1_HUMAN__1727aa_unrelaxed_af2mv3_model_1.pdb, chain B (#1) with DPOA2_HUMAN__WDHD1_HUMAN__1727aa_unrelaxed_af2mv3_model_2.pdb, chain B (#3), sequence alignment score = 5763.8 RMSD between 115 pruned atom pairs is 0.318 angstroms; (across all 1129 pairs: 64.594) > hide #3 models > hide #2 models > select #1/A 4635 atoms, 4731 bonds, 598 residues, 1 model selected > select #1/A#2/A#3/A 13905 atoms, 14193 bonds, 1794 residues, 3 models selected > color (#1 & sel) cornflower blue > select #1/A#2/A#3/A 13905 atoms, 14193 bonds, 1794 residues, 3 models selected > select #1/B#2/B#3/B 26532 atoms, 27069 bonds, 3387 residues, 3 models selected > color (#1 & sel) light sea green > select clear > show #2 models > show #3 models > hide #2 models > hide #3 models > show #2 models > hide #2 models > show #3 models > select #1/A#2/A#3/A 13905 atoms, 14193 bonds, 1794 residues, 3 models selected > color (#1,3 & sel) cornflower blue > select #3/B 8844 atoms, 9023 bonds, 1129 residues, 1 model selected > color sel light sea green > select clear > hide #1 models > save ""/Users/lp212/Dropbox (Cambridge University)/GRANTS/ERG Synergy > REPLITARG/Predictome structures/AND-1/POLA2.cxs"" > close session > open > /Users/lp212/Downloads/PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_1.pdb Chain information for PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_1.pdb #1 --- Chain | Description A | No description available B | No description available > open > /Users/lp212/Downloads/PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_4.pdb Chain information for PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_4.pdb #2 --- Chain | Description A | No description available B | No description available > open > /Users/lp212/Downloads/PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_2.pdb Chain information for PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_2.pdb #3 --- Chain | Description A | No description available B | No description available > ui tool show Matchmaker > matchmaker #2-3 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 PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_1.pdb, chain B (#1) with PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_4.pdb, chain B (#2), sequence alignment score = 5751.8 RMSD between 283 pruned atom pairs is 0.145 angstroms; (across all 1129 pairs: 49.702) Matchmaker PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_1.pdb, chain B (#1) with PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_2.pdb, chain B (#3), sequence alignment score = 5748.2 RMSD between 419 pruned atom pairs is 0.250 angstroms; (across all 1129 pairs: 30.361) > hide #3 models > hide #2 models > show #2 models > ui tool show Matchmaker > matchmaker #2-3 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 PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_1.pdb, chain B (#1) with PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_4.pdb, chain B (#2), sequence alignment score = 5751.8 RMSD between 283 pruned atom pairs is 0.145 angstroms; (across all 1129 pairs: 49.702) Matchmaker PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_1.pdb, chain B (#1) with PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_2.pdb, chain B (#3), sequence alignment score = 5748.2 RMSD between 419 pruned atom pairs is 0.250 angstroms; (across all 1129 pairs: 30.361) > hide #2 models > show #2 models > ui tool show Matchmaker > matchmaker #2/B to #1/B pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_1.pdb, chain B (#1) with PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_4.pdb, chain B (#2), sequence alignment score = 5751.8 RMSD between 283 pruned atom pairs is 0.145 angstroms; (across all 1129 pairs: 49.702) > matchmaker #3/B to #1/B pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_1.pdb, chain B (#1) with PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_2.pdb, chain B (#3), sequence alignment score = 5748.2 RMSD between 419 pruned atom pairs is 0.250 angstroms; (across all 1129 pairs: 30.361) > matchmaker #3/B to #1/B pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_1.pdb, chain B (#1) with PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_2.pdb, chain B (#3), sequence alignment score = 5748.2 RMSD between 419 pruned atom pairs is 0.250 angstroms; (across all 1129 pairs: 30.361) > matchmaker #3/B to #1/B pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_1.pdb, chain B (#1) with PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_2.pdb, chain B (#3), sequence alignment score = 5748.2 RMSD between 419 pruned atom pairs is 0.250 angstroms; (across all 1129 pairs: 30.361) > matchmaker #2/B to #1/B pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_1.pdb, chain B (#1) with PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_4.pdb, chain B (#2), sequence alignment score = 5751.8 RMSD between 283 pruned atom pairs is 0.145 angstroms; (across all 1129 pairs: 49.702) > hide #2 models > ui tool show Matchmaker > matchmaker #2/A to #1/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_1.pdb, chain A (#1) with PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_4.pdb, chain A (#2), sequence alignment score = 963.8 RMSD between 159 pruned atom pairs is 0.585 angstroms; (across all 185 pairs: 6.109) > matchmaker #3/A to #1/A pairing ss Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_1.pdb, chain A (#1) with PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_2.pdb, chain A (#3), sequence alignment score = 966.8 RMSD between 153 pruned atom pairs is 0.614 angstroms; (across all 185 pairs: 6.820) > show #2 models > show #3 models > save ""/Users/lp212/Dropbox (Cambridge University)/GRANTS/ERG Synergy > REPLITARG/Predictome structures/AND-1/Psf2.cxs"" ——— End of log from Sun Oct 8 20:39:28 2023 ——— opened ChimeraX session > open 7pfo 7pfo title: Core human replisome [more info...] Chain information for 7pfo #4 --- Chain | Description | UniProt 2 | DNA replication licensing factor MCM2 | MCM2_HUMAN 1-904 3 | DNA replication licensing factor MCM3 | MCM3_HUMAN 1-808 4 | DNA replication licensing factor MCM4 | MCM4_HUMAN 1-863 5 | DNA replication licensing factor MCM5 | MCM5_HUMAN 1-734 6 | DNA replication licensing factor MCM6 | MCM6_HUMAN 1-821 7 | DNA replication licensing factor MCM7 | MCM7_HUMAN 1-719 A | DNA polymerase epsilon subunit 2 | DPOE2_HUMAN 1-527 B | DNA polymerase epsilon catalytic subunit A | DPOE1_HUMAN 1-2286 C | Cell division control protein 45 homolog,Cell division control protein 45 homolog | CDC45_HUMAN 1-135 136-566 D | DNA replication complex GINS protein PSF1 | PSF1_HUMAN 1-196 E | DNA replication complex GINS protein PSF2 | PSF2_HUMAN 1-185 F | DNA replication complex GINS protein PSF3 | PSF3_HUMAN 1-216 G | DNA replication complex GINS protein SLD5 | SLD5_HUMAN 1-223 H I J | WD repeat and HMG-box DNA-binding protein 1 | WDHD1_HUMAN 1-1129 K | Protein timeless homolog | TIM_HUMAN 1-1208 L | TIMELESS-interacting protein | TIPIN_HUMAN 1-301 M | Leading strand DNA | N | Lagging Strand DNA | Q | Claspin | CLSPN_HUMAN 1-1339 Non-standard residues in 7pfo #4 --- ANP — phosphoaminophosphonic acid-adenylate ester MG — magnesium ion SO4 — sulfate ion ZN — zinc ion > hide #3 models > hide #2 models > show #2 models > hide #2 models > show #2 models > show #3 models > hide #2 models > show #2 models > hide #1 models > show #1 models > hide #2 models > hide #3 models > ui tool show Matchmaker > matchmaker #!4 to #1/A pairing bs Parameters --- Chain pairing | bs 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 PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_1.pdb, chain A (#1) with 7pfo, chain E (#4), sequence alignment score = 906.8 RMSD between 138 pruned atom pairs is 0.860 angstroms; (across all 176 pairs: 2.602) > hide #1#!4 atoms > show #1#!4 cartoons > hide #!4 models > select clear [Repeated 4 time(s)] > select #1/A:39 4 atoms, 3 bonds, 1 residue, 1 model selected > select up 56 atoms, 59 bonds, 8 residues, 1 model selected > view sel > show #!4 models > hide #1 models > select #4/E:39 4 atoms, 3 bonds, 1 residue, 1 model selected > select up 166 atoms, 171 bonds, 22 residues, 1 model selected > show sel atoms > style sel stick Changed 166 atom styles > color sel byhetero > select #4/C:255 11 atoms, 10 bonds, 1 residue, 1 model selected > select up 203 atoms, 206 bonds, 24 residues, 1 model selected > show sel atoms > style sel stick Changed 203 atom styles > color sel byhetero > select clear > select #4/I:473 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 64 atoms, 66 bonds, 8 residues, 1 model selected > show sel atoms > style sel stick Changed 64 atom styles > color sel byhetero > select #4/I:703 11 atoms, 10 bonds, 1 residue, 1 model selected > select up 107 atoms, 111 bonds, 14 residues, 1 model selected > show sel atoms > style sel stick Changed 107 atom styles > color sel byhetero > save ""/Users/lp212/Dropbox (Cambridge University)/GRANTS/ERG Synergy > REPLITARG/Predictome structures/AND-1/Psf2.cxs"" > view #4 clip false > cofr sel > select #4/I:479 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 31 atoms, 31 bonds, 4 residues, 1 model selected > show sel atoms > style sel stick Changed 31 atom styles > color sel byhetero > select clear > ui tool show ""Side View"" > select #4/E:59 11 atoms, 10 bonds, 1 residue, 1 model selected Drag select of 287 atoms, 183 residues, 251 bonds > show sel atoms > style sel stick Changed 1496 atom styles > color sel byhetero > style sel stick Changed 1496 atom styles > style sel stick Changed 1496 atom styles > select clear > select #4/A:227 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 78 atoms, 81 bonds, 9 residues, 1 model selected > select up 4199 atoms, 4310 bonds, 527 residues, 1 model selected > view sel > select clear > select #4/B 6062 atoms, 6180 bonds, 17 pseudobonds, 760 residues, 3 models selected > color (#!4 & sel) hot pink > select clear > select #4/A:16 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 131 atoms, 132 bonds, 16 residues, 1 model selected > select down 8 atoms, 7 bonds, 1 residue, 1 model selected > select #4/A:18 4 atoms, 3 bonds, 1 residue, 1 model selected > select up 12 atoms, 11 bonds, 2 residues, 1 model selected > select add #4/A:17 23 atoms, 21 bonds, 3 residues, 1 model selected > select add #4/A:16 31 atoms, 28 bonds, 4 residues, 1 model selected > select add #4/A:15 40 atoms, 36 bonds, 5 residues, 1 model selected > select add #4/A:20 48 atoms, 43 bonds, 6 residues, 1 model selected > select add #4/A:14 59 atoms, 54 bonds, 7 residues, 1 model selected > select add #4/A:13 64 atoms, 58 bonds, 8 residues, 1 model selected > select add #4/A:12 70 atoms, 63 bonds, 9 residues, 1 model selected > select add #4/A:11 78 atoms, 70 bonds, 10 residues, 1 model selected > show sel target ab > style sel stick Changed 78 atom styles > color sel byhetero > save ""/Users/lp212/Dropbox (Cambridge University)/GRANTS/ERG Synergy > REPLITARG/Predictome structures/AND-1/Psf2.cxs"" ——— End of log from Mon Oct 9 16:37:25 2023 ——— opened ChimeraX session > select clear > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) > set bgColor #ffffff00 Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > lighting simple > lighting soft > hide #!4 atoms > select #4/I 3169 atoms, 3244 bonds, 401 residues, 1 model selected > ui tool show ""Color Actions"" > color sel powder blue target c > color sel light blue target c > color sel sky blue target c > select clear > select #4/2 5613 atoms, 5717 bonds, 9 pseudobonds, 706 residues, 3 models selected > ui tool show ""Color Actions"" > color sel light gray target c > select #4/3 4890 atoms, 4964 bonds, 5 pseudobonds, 622 residues, 3 models selected > color sel light gray target c > select #4/4 4930 atoms, 5013 bonds, 7 pseudobonds, 620 residues, 3 models selected > color sel light gray target c [Repeated 1 time(s)] > select #4/5 4768 atoms, 4840 bonds, 10 pseudobonds, 608 residues, 3 models selected > color sel light gray target c > select #4/6 5015 atoms, 5095 bonds, 7 pseudobonds, 633 residues, 3 models selected > color sel light gray target c > select #4/7 4723 atoms, 4796 bonds, 8 pseudobonds, 596 residues, 3 models selected > color sel light gray target c > select clear > ui tool show ""Model Panel"" > ui tool show ""Side View"" > select #4/B 6062 atoms, 6180 bonds, 17 pseudobonds, 760 residues, 3 models selected > hide sel cartoons > select #4/A 4204 atoms, 4314 bonds, 528 residues, 1 model selected > hide sel cartoons > select #4/K 5215 atoms, 5317 bonds, 2 pseudobonds, 636 residues, 2 models selected > hide sel cartoons > select #4/Q 683 atoms, 693 bonds, 2 pseudobonds, 79 residues, 2 models selected > hide sel cartoons > select #4/L 735 atoms, 750 bonds, 87 residues, 1 model selected > hide sel cartoons > select #4/D 1606 atoms, 1638 bonds, 195 residues, 1 model selected > color sel light gray target c > select #4/E 1431 atoms, 1462 bonds, 176 residues, 1 model selected > color sel light gray target c [Repeated 1 time(s)] > select #4/F 1546 atoms, 1580 bonds, 1 pseudobond, 194 residues, 2 models selected > color sel light gray target c > select clear > select #4/F 1546 atoms, 1580 bonds, 1 pseudobond, 194 residues, 2 models selected > color sel light gray target c [Repeated 2 time(s)] > select #4/G:97 8 atoms, 7 bonds, 1 residue, 1 model selected > select #4/C:255 11 atoms, 10 bonds, 1 residue, 1 model selected > cofr sel > select clear [Repeated 1 time(s)] > select #4/E 1431 atoms, 1462 bonds, 176 residues, 1 model selected > color sel khaki target c > select #4/G 1679 atoms, 1711 bonds, 203 residues, 1 model selected > color sel light gray target c > select clear > select #4/C 4347 atoms, 4439 bonds, 1 pseudobond, 534 residues, 2 models selected > color sel light blue target c > color sel light pink target c > color sel pink target c > select clear > ~pseudobonds Unknown command: ~pseudobonds > ~pseudobond Unknown command: ~pseudobond > hide pseudobonds > view name view1 > save ""/Users/luca/Dropbox (Cambridge University)/GRANTS/ERG Synergy > REPLITARG/Predictome structures/AND-1/Figs/AND1-CMG.png"" width 1848 height > 993 supersample 3 > save ""/Users/luca/Dropbox (Cambridge University)/GRANTS/ERG Synergy > REPLITARG/Predictome structures/AND-1/Psf2.cxs"" ——— End of log from Wed Oct 11 12:40:04 2023 ——— opened ChimeraX session > show #1 models > hide #!4 models > open ""/Users/lp212/Dropbox (Cambridge University)/GRANTS/ERG Synergy > REPLITARG/research/Predictome structures/AND-1/POLA1.cxs"" Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/dialog.py"", line 162, in _qt_safe run(session, ""open "" + "" "".join([FileNameArg.unparse(p) for p in paths]) + ("""" File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 118, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 193, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 458, in collated_open return remember_data_format() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py"", line 428, in remember_data_format models, status = func(*func_args, **func_kw) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core_formats/__init__.py"", line 26, in open return cxs_open(session, data, **kw) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 1001, in open session.restore(stream, path=path, resize_window=resize_window) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 641, in restore use_pickle = stream.peek(1)[0] != ord(b'#') IndexError: index out of range IndexError: index out of range File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 641, in restore use_pickle = stream.peek(1)[0] != ord(b'#') See log for complete Python traceback. OpenGL version: 4.1 Metal - 83.1 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Model Number: MKGT3B/A Chip: Apple M1 Pro Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 8422.141.2 OS Loader Version: 8422.141.2 Software: System Software Overview: System Version: macOS 13.5 (22G74) Kernel Version: Darwin 22.6.0 Time since boot: 1 day, 9 hours, 38 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 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 asttokens: 2.0.8 Babel: 2.10.3 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.8.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.4 ChimeraX-AddH: 2.2 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.6 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.41.4 ChimeraX-AtomicLibrary: 8.0.2 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.7.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.1 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.4 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.5.dev202210110346 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3 ChimeraX-DockPrep: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.9 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.8 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.6 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.1 ChimeraX-MouseModes: 1.1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.1 ChimeraX-PDB: 2.6.8 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 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: 2.7.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.1.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.24.2 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.1 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.3 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 executing: 1.1.1 filelock: 3.7.1 fonttools: 4.37.4 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.33 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 5.0.0 ipykernel: 6.15.3 ipython: 8.4.0 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.1.2 jupyter-client: 7.3.4 jupyter-core: 4.11.1 kiwisolver: 1.4.4 line-profiler: 3.5.1 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.1 matplotlib: 3.5.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.0 networkx: 2.8.5 numexpr: 2.8.3 numpy: 1.23.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.2.0 pip: 22.2.2 pkginfo: 1.8.3 prompt-toolkit: 3.0.31 psutil: 5.9.1 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.12.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2022.4 pyzmq: 24.0.1 qtconsole: 5.3.1 QtPy: 2.2.1 RandomWords: 0.4.0 requests: 2.28.1 scipy: 1.9.0 setuptools: 65.1.1 setuptools-scm: 7.0.5 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 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 stack-data: 0.5.1 tables: 3.7.0 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 typing-extensions: 4.4.0 urllib3: 1.26.12 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 zipp: 3.9.0 }}} " defect assigned normal Input/Output all ChimeraX