id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5883 MemoryError saving map in session chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19042 ChimeraX Version: 1.3.dev202109140730 (2021-09-14 07:30:30 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.3.dev202109140730 (2021-09-14) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open F:/data/paper/Dhr1_K420A_paper/K420A/K420A-90S/SF_Localres_filtered.mrc > F:/data/paper/Dhr1_K420A_paper/K420A/K420A-90S/SG_Localres_filtered.mrc > F:/data/paper/Dhr1_K420A_paper/K420A/K420A-90S/SH_Localres_filtered.mrc Opened SF_Localres_filtered.mrc as #1.1, grid size 448,448,448, pixel 1.33, shown at level 0.0323, step 2, values float32 Opened SG_Localres_filtered.mrc as #1.2, grid size 448,448,448, pixel 1.33, shown at level 0.0341, step 2, values float32 Opened SH_Localres_filtered.mrc as #1.3, grid size 448,448,448, pixel 1.33, shown at level 0.0338, step 2, values float32 > volume #1.1 level 0.01573 > volume #1.2 level 0.01299 > volume #1.3 level 0.01856 > volume #1.1 level 0.01149 > close #1 > open F:/data/paper/Dhr1_K420A_paper/K420A/K420A-90S/K420A-SF-07-refined- > align.pdb Summary of feedback from opening F:/data/paper/Dhr1_K420A_paper/K420A/K420A-90S/K420A-SF-07-refined-align.pdb --- warnings | Ignored bad PDB record found on line 20 GEOMETRY RESTRAINTS LIBRARY: CDL v1.2 Ignored bad PDB record found on line 21 DEVIATIONS FROM IDEAL VALUES. Ignored bad PDB record found on line 22 BOND : 0.009 2.636 224391 Ignored bad PDB record found on line 23 ANGLE : 1.054 19.023 312585 Ignored bad PDB record found on line 24 CHIRALITY : 0.057 0.489 37384 16 messages similar to the above omitted Chain information for K420A-SF-07-refined-align.pdb #1 --- Chain | Description 3A | No description available 3B | No description available 3C | No description available 3D | No description available 3E | No description available 3F | No description available 3G 3H | No description available 5A | No description available 5B | No description available 5C | No description available 5D | No description available 5E | No description available 5F | No description available 5G | No description available 5H | No description available 5I | No description available 5J | No description available 5K | No description available A4 | No description available A5 | No description available A8 | No description available A9 | No description available AE | No description available AF | No description available AG | No description available B1 | No description available B2 | No description available B3 | No description available B6 | No description available B8 | No description available BE | No description available RD | No description available RE | No description available RF | No description available RG | No description available RH | No description available RJ | No description available RK | No description available RN | No description available RO | No description available RP | No description available RQ | No description available RS | No description available RT | No description available RW | No description available SA | No description available SC | No description available SF | No description available SG | No description available SH | No description available SI | No description available SJ | No description available SK | No description available SM | No description available SO | No description available SP | No description available SR | No description available ST | No description available SU | No description available SX | No description available SY | No description available SZ | No description available Sc | No description available Sd | No description available X1 | No description available X2 | No description available > open F:/data/paper/Dhr1_K420A_paper/K420A/K420A-90S/K420A-SG-07-refined- > align.pdb Summary of feedback from opening F:/data/paper/Dhr1_K420A_paper/K420A/K420A-90S/K420A-SG-07-refined-align.pdb --- warnings | Ignored bad PDB record found on line 20 GEOMETRY RESTRAINTS LIBRARY: CDL v1.2 Ignored bad PDB record found on line 21 DEVIATIONS FROM IDEAL VALUES. Ignored bad PDB record found on line 22 BOND : 0.007 0.139 229760 Ignored bad PDB record found on line 23 ANGLE : 1.019 16.616 319746 Ignored bad PDB record found on line 24 CHIRALITY : 0.058 0.451 38145 16 messages similar to the above omitted Chain information for K420A-SG-07-refined-align.pdb #2 --- Chain | Description 3A | No description available 3B | No description available 3C | No description available 3D | No description available 3E | No description available 3F | No description available 3G 3H | No description available 5A | No description available 5B | No description available 5C | No description available 5D | No description available 5E | No description available 5F | No description available 5G | No description available 5H | No description available 5I | No description available 5J | No description available 5K | No description available A4 | No description available A5 | No description available A8 | No description available A9 | No description available AE | No description available AF | No description available AG | No description available B1 | No description available B2 | No description available B3 | No description available B6 | No description available B8 | No description available BE | No description available RD | No description available RE | No description available RF | No description available RG | No description available RH | No description available RJ | No description available RK | No description available RN | No description available RO | No description available RP | No description available RQ | No description available RS | No description available RT | No description available RW | No description available SA | No description available SC | No description available SF | No description available SG | No description available SH | No description available SI | No description available SJ | No description available SK | No description available SM | No description available SO | No description available SP | No description available SR | No description available ST | No description available SU | No description available SX | No description available SY | No description available SZ | No description available Sc | No description available Sd | No description available X1 | No description available X2 | No description available > open F:/data/paper/Dhr1_K420A_paper/K420A/K420A-90S/K420A-SH-07-refined- > align.pdb Summary of feedback from opening F:/data/paper/Dhr1_K420A_paper/K420A/K420A-90S/K420A-SH-07-refined-align.pdb --- warnings | Ignored bad PDB record found on line 20 GEOMETRY RESTRAINTS LIBRARY: CDL v1.2 Ignored bad PDB record found on line 21 DEVIATIONS FROM IDEAL VALUES. Ignored bad PDB record found on line 22 BOND : 0.011 0.214 231980 Ignored bad PDB record found on line 23 ANGLE : 1.146 17.704 322748 Ignored bad PDB record found on line 24 CHIRALITY : 0.064 0.607 38488 16 messages similar to the above omitted Chain information for K420A-SH-07-refined-align.pdb #3 --- Chain | Description 3A | No description available 3B | No description available 3C | No description available 3D | No description available 3E | No description available 3F | No description available 3G 3H | No description available 5A | No description available 5B | No description available 5C | No description available 5D | No description available 5E | No description available 5F | No description available 5G | No description available 5H | No description available 5I | No description available 5J | No description available 5K | No description available A4 | No description available A5 | No description available A8 | No description available A9 | No description available AE | No description available AF | No description available AG | No description available B1 | No description available B2 | No description available B3 | No description available B6 | No description available B8 | No description available BE | No description available RD | No description available RE | No description available RF | No description available RG | No description available RH | No description available RJ | No description available RK | No description available RN | No description available RO | No description available RP | No description available RQ | No description available RS | No description available RT | No description available RU | No description available RW | No description available SA | No description available SC | No description available SF | No description available SG | No description available SH | No description available SI | No description available SJ | No description available SK | No description available SM | No description available SO | No description available SP | No description available SR | No description available ST | No description available SU | No description available SX | No description available SY | No description available SZ | No description available Sc | No description available Sd | No description available X1 | No description available X2 | No description available > open F:/data/paper/Dhr1_K420A_paper/K420A/postprocess_mrc/GH-SG.mrc > F:/data/paper/Dhr1_K420A_paper/K420A/postprocess_mrc/GH-SH.mrc > F:/data/paper/Dhr1_K420A_paper/K420A/postprocess_mrc/SI-A1cleaved.mrc Opened GH-SG.mrc as #4.1, grid size 448,448,448, pixel 1.33, shown at level 0.0194, step 2, values float32 Opened GH-SH.mrc as #4.2, grid size 448,448,448, pixel 1.33, shown at level 0.0207, step 2, values float32 Opened SI-A1cleaved.mrc as #4.3, grid size 448,448,448, pixel 1.33, shown at level 0.0207, step 2, values float32 > select #1 216553 atoms, 224395 bonds, 191 pseudobonds, 24724 residues, 3 models selected > select #2 221784 atoms, 229760 bonds, 173 pseudobonds, 25192 residues, 3 models selected > select #1 216553 atoms, 224395 bonds, 191 pseudobonds, 24724 residues, 3 models selected > show sel cartoons > hide sel atoms > select #2 221784 atoms, 229760 bonds, 173 pseudobonds, 25192 residues, 3 models selected > show sel cartoons > hide sel atoms > select #3 223963 atoms, 231980 bonds, 174 pseudobonds, 25464 residues, 3 models selected > show sel cartoons > hide sel atoms > hide #!4.3 models > hide #!4.2 models > hide #!4.1 models > hide #!1 models > show #!1 models > hide #!2 models > hide #!3 models > select #1 216553 atoms, 224395 bonds, 191 pseudobonds, 24724 residues, 3 models selected > color #1 #f5f2f1 > select clear > ui tool show ""Color Actions"" > set bgColor white > select #1 /SA :1-608 :609-1144 22054 atoms, 24663 bonds, 10 pseudobonds, 1035 residues, 2 models selected > color #1 /SA :1-608 forest green color #1 /SA :609-1144 gold Invalid ""color"" argument: Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' > color #1 /SA :1-608 forest green > color #1 /SA :609-1144 gold > show #!4.1 models > hide #!4.1 models > color #4.1 #bb22bb models > color #4.1 #ff55ff models > color #4.1 #f5f2f1 models > select #2 221784 atoms, 229760 bonds, 173 pseudobonds, 25192 residues, 3 models selected > show #!2 models > color #4.1 #f5f1ef models > color #4.1 #f5f3ef models > color #4.1 #b5b5b5 models > color #2 #f5e9dd > color #2 #f5efea > color #2 #f5f0e9 > color #2 #ff55ff > color #2 #f5f2f1 > select #3 223963 atoms, 231980 bonds, 174 pseudobonds, 25464 residues, 3 models selected > show #!3 models > color #2 #f5f0ee > color #2 #f5f1ea > color #2 #f5efec > color #2 #ff55ee > color #2 #ff55ff > color #2 #f5f2f1 > color #1 /SA :609-1144 gold > color #3 #f5f0ec > color #3 #ff55ff > color #3 #f5f2f1 > select clear > color #1 /SA :1-608 forest green > color #1 /SA :609-1144 gold > color #2 /SA :1-608 forest green > color #2 /SA :609-1144 gold > color #3 /SA :1-608 forest green > color #3 /SA :609-1144 gold > hide #!3 models > show #!3 models > hide #!3 models > hide #!2 models > hide #!1 models > show #!1 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > select #1 /SA :1-608:609-1144 22054 atoms, 24663 bonds, 10 pseudobonds, 1035 residues, 2 models selected > show #!1 models > hide #!2 models > close #4.3 > open F:/data/paper/Dhr1_K420A_paper/K420A/postprocess_mrc/SF.mrc Opened SF.mrc as #5, grid size 448,448,448, pixel 1.33, shown at level 0.0181, step 2, values float32 > volume #5 level 0.01157 > volume #5 level 0.009273 > hide #!4.1 models > hide #!4 models > ui tool show ""Surface Color"" > ui tool show ""Color Zone"" > color zone #5 near sel distance 8 > color zone #5 near sel distance 10 [Repeated 1 time(s)] > volume splitbyzone #5 Opened SF.mrc 0 as #6.1, grid size 448,448,448, pixel 1.33, shown at level 0.00927, step 1, values float32 Opened SF.mrc 1 as #6.2, grid size 448,448,448, pixel 1.33, shown at level 0.00927, step 1, values float32 Opened SF.mrc 2 as #6.3, grid size 448,448,448, pixel 1.33, shown at level 0.00927, step 1, values float32 > hide #!6 models > show #!6 models > hide #!6.1 models > hide #!6.3 models > show #!6.3 models > hide #!6.2 models > show #!6.2 models > hide #!1 models > show #!6.1 models > hide #!6.1 models > hide #!6.2 models > color zone #5 near sel distance 18 > color zone #5 near sel distance 8 > show #!5 models > color zone #5 near sel distance 5 > volume splitbyzone #5 Opened SF.mrc 0 as #7.1, grid size 448,448,448, pixel 1.33, shown at level 0.00927, step 1, values float32 Opened SF.mrc 1 as #7.2, grid size 448,448,448, pixel 1.33, shown at level 0.00927, step 1, values float32 Opened SF.mrc 2 as #7.3, grid size 448,448,448, pixel 1.33, shown at level 0.00927, step 1, values float32 > hide #!7.1 models > hide #!7.2 models > show #!7.2 models > hide #!7.3 models > hide #!7 models > show #!7 models > hide #!7 models > hide #!7.2 models > hide #!6.3 models > show #!7.2 models > show #!7.3 models > show #!1 models > hide #!1 models > hide #!6 models > show #!2 models > hide #!7.2 models > hide #!7.3 models > hide #!7 models > show #!4.1 models > select #2 /SA :1-608:609-1144 23117 atoms, 25848 bonds, 12 pseudobonds, 1085 residues, 2 models selected > volume #4.1 level 0.0091 > color zone #4.1 near sel distance 5 > volume splitbyzone #4.1 Opened GH-SG.mrc 0 as #8.1, grid size 448,448,448, pixel 1.33, shown at level 0.0091, step 1, values float32 Opened GH-SG.mrc 1 as #8.2, grid size 448,448,448, pixel 1.33, shown at level 0.0091, step 1, values float32 Opened GH-SG.mrc 2 as #8.3, grid size 448,448,448, pixel 1.33, shown at level 0.0091, step 1, values float32 > hide #!8.1 models > hide #!4 models > show #!4 models > hide #!2 models > show #!7.2 models > show #!7.3 models > hide #!7.2 models > show #!7.2 models > hide #!7.2 models > show #!7.2 models > hide #!7.2 models > show #!7.2 models > hide #!7.2 models > show #!7.2 models > hide #!7.2 models > show #!7.2 models > hide #!7.2 models > show #!7.2 models > hide #!7.2 models > show #!7.2 models > hide #!7.3 models > show #!7.3 models > hide #!7.3 models > show #!7.3 models > hide #!7.3 models > show #!7.3 models > hide #!7.3 models > show #!7.3 models > hide #!7.3 models > show #!7.3 models > hide #!7.3 models > show #!7.3 models > hide #!7.3 models > show #!7.3 models > hide #!7.3 models > show #!7.3 models > hide #!7.3 models > show #!7.3 models > hide #!7.3 models > show #!7.3 models > hide #!7.3 models > show #!7.3 models > show #!4.1 models > hide #!4.1 models > show #!4.1 models > hide #!4.1 models > show #!8.1 models > hide #!8.1 models > hide #!7.2 models > show #!7.2 models > hide #!7.2 models > show #!7.2 models > hide #!7.2 models > hide #!7.3 models > show #!7.3 models > show #!7.2 models > hide #!8.2 models > hide #!8.3 models > show #!8.2 models > hide #!8.2 models > show #!8.2 models > hide #!8.2 models > show #!8.2 models > hide #!8.2 models > show #!8.2 models > hide #!8.2 models > show #!8.2 models > hide #!8.2 models > show #!1 models > hide #!1 models > show #!3 models > hide #!3 models > show #!3 models > select #3/RU 2179 atoms, 2220 bonds, 1 pseudobond, 272 residues, 2 models selected > show #!2 models > hide #!2 models > show #!2 models > hide #!3 models > hide #!7.3 models > show #!7.3 models > hide #!7.3 models > show #!7.3 models > hide #!7.3 models > show #!7.3 models > hide #!7.3 models > show #!7.3 models > hide #!7.3 models > show #!8.1 models > hide #!8.1 models > show #!8.3 models > hide #!8.3 models > show #!8.3 models > show #!3 models > hide #!3 models > show #!3 models > open F:/data/paper/Dhr1_K420A_paper/K420A/K420A-90S/K420A-SI-07-refined- > align.pdb Summary of feedback from opening F:/data/paper/Dhr1_K420A_paper/K420A/K420A-90S/K420A-SI-07-refined-align.pdb --- warnings | Ignored bad PDB record found on line 20 GEOMETRY RESTRAINTS LIBRARY: CDL v1.2 Ignored bad PDB record found on line 21 DEVIATIONS FROM IDEAL VALUES. Ignored bad PDB record found on line 22 BOND : 0.009 0.207 239586 Ignored bad PDB record found on line 23 ANGLE : 1.093 18.055 333032 Ignored bad PDB record found on line 24 CHIRALITY : 0.061 0.815 39672 16 messages similar to the above omitted End residue of secondary structure not found: HELIX 15 15 ALASF 247 ALASF 255 1 9 Chain information for K420A-SI-07-refined-align.pdb #9 --- Chain | Description 3A | No description available 3B | No description available 3C | No description available 3D | No description available 3E | No description available 3F | No description available 3G 3H | No description available 5A | No description available 5B | No description available 5C | No description available 5D | No description available 5E | No description available 5F | No description available 5G | No description available 5H | No description available 5I | No description available 5J | No description available 5K | No description available A4 | No description available A5 | No description available A8 | No description available A9 | No description available AE | No description available AF | No description available AG | No description available B1 | No description available B2 | No description available B3 | No description available B6 | No description available B8 | No description available BE | No description available RD | No description available RE | No description available RF | No description available RG | No description available RH | No description available RJ | No description available RK | No description available RN | No description available RO | No description available RP | No description available RQ | No description available RS | No description available RT | No description available RU | No description available RW | No description available RZ | No description available SA | No description available SC | No description available SF | No description available SG | No description available SH | No description available SI | No description available SJ | No description available SK | No description available SM | No description available SO | No description available SP | No description available SR | No description available ST | No description available SU | No description available SX | No description available SY | No description available SZ | No description available Sc | No description available Sd | No description available X1 | No description available X2 | No description available > open F:/data/paper/Dhr1_K420A_paper/K420A/postprocess_mrc/SI-A1cleaved.mrc Opened SI-A1cleaved.mrc as #10, grid size 448,448,448, pixel 1.33, shown at level 0.0207, step 2, values float32 > color #10 /SA :1-608 forest green > color #10 /SA :609-1144 gold > hide #!10 models > show #!10 models > select #10 2 models selected > hide #!2-3,9 atoms > show #!2-3,9 cartoons > hide #!8.3 models > hide #!8.2 models > color #9 /SA :609-1144 gold > color #9 /SA :1-608 forest green > hide #!7.2 models > show #!10 models > color #10 #fffaf8 models > color #9 #fff7f2 > color #9 #fff7f4 > color #9 #fffcf7 > color #9 white > color #9 #ff55ff > color #9 #f5f2f1 > hide #!10 models > hide #!9 models > hide #!7 models > hide #!2 models > hide #!3 models > show #!9 models > color #9 /SA :1-608 forest green > color #9 /SA :609-1144 gold > show #!10 models > color #9 /SA :609-1144 gold color #9 /SA :1-608 forest green Invalid ""color"" argument: Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' > color #9 /SA :609-1144 gold color #9 /SA :1-608 forest green Invalid ""color"" argument: Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' > color #9 /SA :609-1144 gold color #9 /SA :1-608 forest green Invalid ""color"" argument: Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' > color #9 /SA :1-608 forest green > color #9 /SA :609-1144 gold No atoms selected for color zoning > select #9 231406 atoms, 239557 bonds, 184 pseudobonds, 26440 residues, 3 models selected > hide #!10 models > color #9 /SA :1-608 forest green > color #9 /SA :609-1144 gold > ~select #9 Nothing selected > color #9 /SA :609-1144 gold [Repeated 1 time(s)] > color #9 /SA :1-608 forest green > color #9 /SA :609-1144 gold > select #9 /SA :1-608 :609-1144 23252 atoms, 26002 bonds, 11 pseudobonds, 1091 residues, 2 models selected > color zone #10 near sel distance 8 > show #!10 models > volume splitbyzone #10 Opened SI-A1cleaved.mrc 0 as #11.1, grid size 448,448,448, pixel 1.33, shown at level 0.0207, step 1, values float32 Opened SI-A1cleaved.mrc 1 as #11.2, grid size 448,448,448, pixel 1.33, shown at level 0.0207, step 1, values float32 Opened SI-A1cleaved.mrc 2 as #11.3, grid size 448,448,448, pixel 1.33, shown at level 0.0207, step 1, values float32 > hide #!11.1 models > hide #!9 models > show #!8.2 models > hide #!8.2 models > show #!8.2 models > hide #!8.2 models > show #!8.2 models > hide #!8.2 models > show #!8.2 models > hide #!8.2 models > show #!8.2 models > show #!8.3 models > hide #!8.3 models > show #!8.3 models > hide #!8.3 models > show #!8.3 models > hide #!8.3 models > show #!8.3 models > hide #!8.3 models > show #!8.3 models > hide #!8.3 models > show #!8.3 models > hide #!8.3 models > show #!8.3 models > hide #!8.2 models > hide #!8.3 models > hide #!11.3 models > hide #!11.2 models > show #!3 models > select #3 /SA :11-15 :1139-1144 234 atoms, 260 bonds, 11 residues, 1 model selected > show #!2 models > hide #!3 models > select #2 /SA :11-15 :1139-1144 234 atoms, 260 bonds, 11 residues, 1 model selected > show #!1 models > select #1 /SA :11-15 :1139-1144 234 atoms, 260 bonds, 11 residues, 1 model selected > show #!3 models > hide #!2 models > hide #!3 models > hide #!1 models > show #!2 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > open F:/data/paper/Dhr1_K420A_paper/K420A/K420A-90S/K420A-SM-07-refined- > align.pdb Summary of feedback from opening F:/data/paper/Dhr1_K420A_paper/K420A/K420A-90S/K420A-SM-07-refined-align.pdb --- warnings | Ignored bad PDB record found on line 20 GEOMETRY RESTRAINTS LIBRARY: CDL v1.2 Ignored bad PDB record found on line 21 DEVIATIONS FROM IDEAL VALUES. Ignored bad PDB record found on line 22 BOND : 0.012 0.156 95003 Ignored bad PDB record found on line 23 ANGLE : 1.151 20.369 135622 Ignored bad PDB record found on line 24 CHIRALITY : 0.064 0.491 16561 16 messages similar to the above omitted Start residue of secondary structure not found: HELIX 69 69 ASNST 103 ILEST 119 1 17 Start residue of secondary structure not found: HELIX 109 109 GLYRG 75 METRG 80 1 6 Start residue of secondary structure not found: HELIX 110 110 ASPRG 90 THRRG 98 1 9 Start residue of secondary structure not found: HELIX 111 111 PHERG 134 PHERG 137 1 4 Start residue of secondary structure not found: HELIX 112 112 VALRG 142 LEURG 145 1 4 71 messages similar to the above omitted Chain information for K420A-SM-07-refined-align.pdb #12 --- Chain | Description 3A | No description available 5E | No description available 5G | No description available 5H | No description available 5K | No description available RJ | No description available RK | No description available RQ | No description available RT | No description available RU | No description available RZ | No description available SA | No description available SC | No description available SF | No description available SG | No description available SH | No description available SI | No description available SJ | No description available SK | No description available SM | No description available SO | No description available SP | No description available SR | No description available ST | No description available SU | No description available SX | No description available SY | No description available SZ | No description available Sa | No description available Sc | No description available Sd | No description available X1 | No description available X2 | No description available > select #12 76905 atoms, 81345 bonds, 28 pseudobonds, 7271 residues, 3 models selected > hide sel atoms > show sel cartoons > color #12 #b5b5b5 > select #12 /SA :11-15 :1139-1144 234 atoms, 260 bonds, 11 residues, 1 model selected > hide #!2 models > show #!2 models > hide #!1 models > hide #!2 models > show #!1 models > show #!2 models > hide #!2 models > hide #!1 models > hide #!4 models > hide #!8 models > show #!8.2 models > hide #!8.2 models > hide #!12 models > show #!11.2 models > show #!11.3 models > show #!1 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 > show #!3 models > select #3/RU 2179 atoms, 2220 bonds, 1 pseudobond, 272 residues, 2 models selected > hide #!3 models > show #!3 models > select #3 223963 atoms, 231980 bonds, 174 pseudobonds, 25464 residues, 3 models selected > select #2 221784 atoms, 229760 bonds, 173 pseudobonds, 25192 residues, 3 models selected > select #3 223963 atoms, 231980 bonds, 174 pseudobonds, 25464 residues, 3 models selected > hide #!1 models > hide #!3 models > show #!11.1 models > hide #!11.3 models > hide #!11.2 models > show #!11.3 models > show #!11.2 models > select #11.1 2 models selected > transparency sel 50 > select clear > hide #!11.1 models > show #!11.1 models > hide #!11.1 models > show #!11.1 models > hide #!11.2 models > hide #!11.3 models > show #!11.2 models > show #!11.3 models > hide #!11.3 models > hide #!11.2 models > hide #!11.1 models > show #!8.2 models > show #!8.3 models > show #!8.1 models > show #!11.3 models > hide #!11.3 models > show #!11.3 models > hide #!11.3 models > show #!11.3 models > hide #!11.3 models > show #!11.3 models > hide #!11.3 models > show #!11.2 models > hide #!11.2 models > hide #!11 models > show #!11 models > hide #!8 models > show #!8 models > hide #!8.1 models > show #!8.1 models > hide #!8.1 models > show #!8.1 models > hide #!8.1 models > show #!8.1 models > hide #!8.1 models > show #!8.1 models > hide #!8.1 models > show #!8.1 models > hide #!8.1 models > show #!8.1 models > show #!2 models > hide #!8.1 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!2 models > show #!8.1 models > select #8.1 2 models selected > transparency sel 50 > volume #4.1 level 0.02074 > volume #4.1 level 0.03238 > volume #4.1 level 0.008238 > volume #4.1 level 0.01039 > volume #4.1 level 0.006944 > hide #!8 models > show #!8 models > hide #!8.1 models > show #!8.1 models > hide #!8.1 models > show #!8.1 models > hide #!8.1 models > show #!8.1 models > hide #!8.1 models > save ""F:/data/paper/Dhr1_K420A_paper/awd_figure/figure3/5domain_central > domain/SG_3central.png"" width 861 height 657 supersample 3 > transparentBackground true > show #!8.1 models > hide #!8.2 models > hide #!8.3 models > select clear > save ""F:/data/paper/Dhr1_K420A_paper/awd_figure/figure3/5domain_central > domain/SG_all.png"" width 861 height 657 supersample 3 > save ""F:/data/paper/Dhr1_K420A_paper/awd_figure/figure3/5domain_central > domain/SG_all.png"" width 861 height 657 supersample 3 transparentBackground > true > hide #!8 models > hide #!8.1 models > show #!8.1 models > transparency #8.1.1 0 > transparency #8.1.1 50 > show #!8.2 models > show #!8.3 models > show #!3 models > volume #!8.1-3 showOutlineBox true > hide #!8.3 models > hide #!8.2 models > hide #!8.1 models > hide #!8 models > hide #!3 models > show #!3 models > hide #!4.1 models > show #!4.2 models > color #4.2 #fffaf8 models > select #3/RU 2179 atoms, 2220 bonds, 1 pseudobond, 272 residues, 2 models selected > color (#!3 & sel) cyan > volume #4.1 level 0.006513 > volume #4.2 level 0.0101 > color #3 /RU cyan > select #3 /RU/SA:1-608:609-1144 25296 atoms, 28068 bonds, 13 pseudobonds, 1357 residues, 2 models selected > color zone #4.2 near sel distance 8 > volume splitbyzone #4.2 Opened GH-SH.mrc 0 as #13.1, grid size 448,448,448, pixel 1.33, shown at level 0.0101, step 1, values float32 Opened GH-SH.mrc 1 as #13.2, grid size 448,448,448, pixel 1.33, shown at level 0.0101, step 1, values float32 Opened GH-SH.mrc 2 as #13.3, grid size 448,448,448, pixel 1.33, shown at level 0.0101, step 1, values float32 Opened GH-SH.mrc 3 as #13.4, grid size 448,448,448, pixel 1.33, shown at level 0.0101, step 1, values float32 > hide #!13.1 models > show #!13.1 models > hide #!13.1 models > show #!13.1 models > hide #!13.1 models > hide #!3 models > show #!13.1 models > select #13.1 2 models selected > transparency sel 50 > hide #!13.4 models > hide #!13.3 models > hide #!13.2 models > select clear > save ""F:/data/paper/Dhr1_K420A_paper/awd_figure/figure3/5domain_central > domain/SH_all.png"" width 861 height 657 supersample 3 > hide #!13.1 models > show #!13.2 models > show #!13.3 models > show #!13.4 models > save ""F:/data/paper/Dhr1_K420A_paper/awd_figure/figure3/5domain_central > domain/SH_3central.png"" width 861 height 657 supersample 3 > show #!11.1 models > hide #!11.1 models > show #!9 models > hide #!13.2 models > hide #!13.3 models > hide #!13.4 models > hide #!13 models > hide #!9 models > show #!9 models > color #9 /RU cyan /RZ red Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color #9 /RU cyan > color #9 /RZ red > undo > color #9 /RZ:90-136 red > show #!10 models > volume #11.1 level 0.01579 > volume #10 level 0.007355 > volume #10 level 0.01329 > volume #10 level 0.009828 No atoms selected for color zoning > select #9 /RZ:90-136/SA:1-608:609-1144/RU 25868 atoms, 28663 bonds, 11 pseudobonds, 1421 residues, 2 models selected > color zone #10 near sel distance 8 > volume splitbyzone #10 Opened SI-A1cleaved.mrc 0 as #14.1, grid size 448,448,448, pixel 1.33, shown at level 0.00983, step 1, values float32 Opened SI-A1cleaved.mrc 1 as #14.2, grid size 448,448,448, pixel 1.33, shown at level 0.00983, step 1, values float32 Opened SI-A1cleaved.mrc 2 as #14.3, grid size 448,448,448, pixel 1.33, shown at level 0.00983, step 1, values float32 Opened SI-A1cleaved.mrc 3 as #14.4, grid size 448,448,448, pixel 1.33, shown at level 0.00983, step 1, values float32 Opened SI-A1cleaved.mrc 4 as #14.5, grid size 448,448,448, pixel 1.33, shown at level 0.00983, step 1, values float32 > hide #!14.2 models > show #!14.2 models > select #14.1 2 models selected > transparency sel 50 > select clear > hide #!14.1 models > hide #!9 models > save ""F:/data/paper/Dhr1_K420A_paper/awd_figure/figure3/5domain_central > domain/SI_3central.png"" width 861 height 657 supersample 3 > transparentBackground true > hide #!14.5 models > hide #!14.4 models > hide #!14.3 models > hide #!14.2 models > show #!14.1 models > save ""F:/data/paper/Dhr1_K420A_paper/awd_figure/figure3/5domain_central > domain/SI_all.png"" width 861 height 657 supersample 3 transparentBackground > true > hide #!14.1 models > hide #!14 models > hide #!11 models > show #!8.1 models > transparency #8.1.1 0 > transparency #8.1.1 50 > save ""F:/data/paper/Dhr1_K420A_paper/awd_figure/figure3/5domain_central > domain/SH_allv1.png"" width 861 height 657 supersample 3 > hide #!8.1 models > show #!8.2 models > show #!8.3 models > save ""F:/data/paper/Dhr1_K420A_paper/awd_figure/figure3/5domain_central > domain/SHv1_3central.png"" width 861 height 657 supersample 3 > save ""F:/data/paper/Dhr1_K420A_paper/awd_figure/figure3/5domain_central > domain/SHv1_3central.png"" width 861 height 657 supersample 3 > transparentBackground true > hide #!8.2 models > hide #!8.3 models > show #!8.1 models > save ""F:/data/paper/Dhr1_K420A_paper/awd_figure/figure3/5domain_central > domain/SH_allv1.png"" width 861 height 657 supersample 3 > transparentBackground true > hide #!8 models > hide #!8.1 models > show #!13.2 models > show #!13.3 models > show #!13.4 models > save ""F:/data/paper/Dhr1_K420A_paper/awd_figure/figure3/5domain_central > domain/SHv1_3central.png"" width 861 height 657 supersample 3 > show #!13.1 models > hide #!13.2 models > hide #!13.3 models > hide #!13.4 models > transparency #13.1.1 0 > transparency #13.1.1 50 > save ""F:/data/paper/Dhr1_K420A_paper/awd_figure/figure3/5domain_central > domain/SH_allv1.png"" width 861 height 657 supersample 3 > transparentBackground true > hide #!13.1 models > show #!13.2 models > show #!13.3 models > show #!13.4 models > save ""F:/data/paper/Dhr1_K420A_paper/awd_figure/figure3/5domain_central > domain/SHv1_3central.png"" width 861 height 657 supersample 3 > save ""F:/data/paper/Dhr1_K420A_paper/awd_figure/figure3/5domain_central > domain/SH_3central.png"" width 861 height 657 supersample 3 > transparentBackground true > hide #!13.4 models > hide #!13.3 models > hide #!13.2 models > show #!13.1 models > save ""F:/data/paper/Dhr1_K420A_paper/awd_figure/figure3/5domain_central > domain/SH_allv1.png"" width 861 height 657 supersample 3 > transparentBackground true > hide #!13.1 models > show #!13.2 models > show #!13.3 models > show #!13.4 models > save ""F:/data/paper/Dhr1_K420A_paper/awd_figure/figure3/5domain_central > domain/SHv1_3central.png"" width 861 height 657 supersample 3 > transparentBackground true > show #!3 models > hide #!13.2 models > hide #!13.3 models > hide #!13.4 models > save F:/data/paper/Dhr1_K420A_paper/awd_figure/fig3_5centrapmap.cxs Traceback (most recent call last): File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\core\session.py"", line 281, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\map\session.py"", line 200, in take_snapshot data = state_from_grid_data(self.grid_data, session_path = session.session_file_path, File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\map\session.py"", line 316, in state_from_grid_data s['array'] = dt.matrix().tobytes() MemoryError The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\core\session.py"", line 260, in discovery self.processed[key] = self.process(obj, parents) File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\core\session.py"", line 284, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'models' -> -> 'surface' -> 'SI-A1cleaved.mrc 0' -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\core\session.py"", line 882, in save session.save(output, version=version, include_maps=include_maps) File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\core\session.py"", line 611, in save mgr.discovery(self._state_containers) File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\core\session.py"", line 262, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'models' -> -> 'surface' -> 'SI-A1cleaved.mrc 0' -> : Error while saving session data for 'models' -> -> 'surface' -> 'SI-A1cleaved.mrc 0' -> ValueError: error processing: 'models' -> -> 'surface' -> 'SI-A1cleaved.mrc 0' -> : Error while saving session data for 'models' -> -> 'surface' -> 'SI-A1cleaved.mrc 0' -> File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\core\session.py"", line 262, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\core\session.py"", line 281, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\map\session.py"", line 200, in take_snapshot data = state_from_grid_data(self.grid_data, session_path = session.session_file_path, File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\map\session.py"", line 316, in state_from_grid_data s['array'] = dt.matrix().tobytes() MemoryError The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\core\session.py"", line 260, in discovery self.processed[key] = self.process(obj, parents) File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\core\session.py"", line 284, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'models' -> -> 'surface' -> 'SI-A1cleaved.mrc 0' -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 116, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 51, in display run(session, cmd) File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\core\commands\run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\save_command\cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\save_command\cmd.py"", line 89, in provider_save saver_info.save(session, path, **provider_kw) File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\core_formats\\__init__.py"", line 84, in save return cxs_save(session, path, **kw) File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\core\session.py"", line 882, in save session.save(output, version=version, include_maps=include_maps) File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\core\session.py"", line 611, in save mgr.discovery(self._state_containers) File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\core\session.py"", line 262, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'models' -> -> 'surface' -> 'SI-A1cleaved.mrc 0' -> : Error while saving session data for 'models' -> -> 'surface' -> 'SI-A1cleaved.mrc 0' -> ValueError: error processing: 'models' -> -> 'surface' -> 'SI-A1cleaved.mrc 0' -> : Error while saving session data for 'models' -> -> 'surface' -> 'SI-A1cleaved.mrc 0' -> File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\core\session.py"", line 262, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. > save F:/data/paper/Dhr1_K420A_paper/awd_figure/figure3/figmap.cxs Traceback (most recent call last): File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\core\session.py"", line 281, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\map\session.py"", line 200, in take_snapshot data = state_from_grid_data(self.grid_data, session_path = session.session_file_path, File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\map\session.py"", line 316, in state_from_grid_data s['array'] = dt.matrix().tobytes() MemoryError The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\core\session.py"", line 260, in discovery self.processed[key] = self.process(obj, parents) File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\core\session.py"", line 284, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'models' -> -> 'surface' -> 'SI-A1cleaved.mrc 0' -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\core\session.py"", line 882, in save session.save(output, version=version, include_maps=include_maps) File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\core\session.py"", line 611, in save mgr.discovery(self._state_containers) File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\core\session.py"", line 262, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'models' -> -> 'surface' -> 'SI-A1cleaved.mrc 0' -> : Error while saving session data for 'models' -> -> 'surface' -> 'SI-A1cleaved.mrc 0' -> ValueError: error processing: 'models' -> -> 'surface' -> 'SI-A1cleaved.mrc 0' -> : Error while saving session data for 'models' -> -> 'surface' -> 'SI-A1cleaved.mrc 0' -> File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\core\session.py"", line 262, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\core\session.py"", line 281, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\map\session.py"", line 200, in take_snapshot data = state_from_grid_data(self.grid_data, session_path = session.session_file_path, File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\map\session.py"", line 316, in state_from_grid_data s['array'] = dt.matrix().tobytes() MemoryError The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\core\session.py"", line 260, in discovery self.processed[key] = self.process(obj, parents) File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\core\session.py"", line 284, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'models' -> -> 'surface' -> 'SI-A1cleaved.mrc 0' -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 116, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 51, in display run(session, cmd) File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\core\commands\run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\save_command\cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\save_command\cmd.py"", line 89, in provider_save saver_info.save(session, path, **provider_kw) File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\core_formats\\__init__.py"", line 84, in save return cxs_save(session, path, **kw) File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\core\session.py"", line 882, in save session.save(output, version=version, include_maps=include_maps) File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\core\session.py"", line 611, in save mgr.discovery(self._state_containers) File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\core\session.py"", line 262, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'models' -> -> 'surface' -> 'SI-A1cleaved.mrc 0' -> : Error while saving session data for 'models' -> -> 'surface' -> 'SI-A1cleaved.mrc 0' -> ValueError: error processing: 'models' -> -> 'surface' -> 'SI-A1cleaved.mrc 0' -> : Error while saving session data for 'models' -> -> 'surface' -> 'SI-A1cleaved.mrc 0' -> File ""D:\program\ChimeraX 1.3.dev202109140730\bin\lib\site- packages\chimerax\core\session.py"", line 262, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 461.43 OpenGL renderer: GeForce MX450/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: LENOVO Model: 82NC OS: Microsoft Windows 10 家庭中文版 (Build 19042) Memory: 16,952,647,680 MaxProcessMemory: 137,438,953,344 CPU: 8 11th Gen Intel(R) Core(TM) i5-11300H @ 3.10GHz 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: 2021.5.30 cftime: 1.5.0 chardet: 4.0.0 ChimeraX-AddCharge: 1.1.4 ChimeraX-AddH: 2.1.10 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.29.1 ChimeraX-AtomicLibrary: 4.1.4 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: 2.5.3 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: 2.1 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.4.1 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3.dev202109140730 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.1 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: 2.1.1 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: 2.0.1 ChimeraX-MDcrds: 2.5 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 ChimeraX-ModelPanel: 1.1.1 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: 2.6.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.1 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 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 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: 2.4.3 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 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: 1.12.1 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: 0.10.0 Cython: 0.29.24 decorator: 5.1.0 distlib: 0.3.2 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.4.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.20 imagecodecs: 2021.4.28 imagesize: 1.2.0 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: 4.7.1 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: 2.7.3 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.0 ParmEd: 3.2.0 parso: 0.8.2 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.20 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: 2.4.7 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.1 pytz: 2021.1 pywin32: 228 pyzmq: 22.2.1 qtconsole: 5.1.1 QtPy: 1.11.1 RandomWords: 0.3.0 requests: 2.25.1 scipy: 1.7.1 setuptools: 58.0.4 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.1.0 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: 5.1.0 urllib3: 1.26.6 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 WMI: 1.5.1 }}} " defect closed normal Sessions limitation all ChimeraX