id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20198 lighting full: glTexImage2D: out of memory andysen@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.26200 ChimeraX Version: 1.11 (2025-12-17 06:45:39 UTC) Description Replace this text with list of actions that caused this problem to occur Log: UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. > open > C:\Users\andys\OneDrive\Documents\baseplate\main_baseplate\all_base3.cxs > format session Opened flip_base.mrc as #9, grid size 512,512,512, pixel 1.39, shown at level 0.272, step 1, values float32 Log from Wed Dec 4 16:01:10 2024UCSF ChimeraX version: 1.8rc202406102315 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open > /Users/aninditosen/Documents/P1/baseplate/main_baseplate/full_baseplate.cxs Opened flip_base.mrc as #9, grid size 512,512,512, pixel 1.39, shown at level 0.272, step 1, values float32 Log from Mon Dec 2 17:54:21 2024UCSF ChimeraX version: 1.8rc202406102315 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open > /Users/aninditosen/Documents/P1/baseplate/main_baseplate/all_baseplate_tube_sheath4.cxs Opened flip_base.mrc as #9, grid size 512,512,512, pixel 1.39, shown at level 0.272, step 1, values float32 Log from Mon Dec 2 16:19:56 2024UCSF ChimeraX version: 1.8rc202406102315 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open > /Users/aninditosen/Documents/P1/baseplate/main_baseplate/all_baseplate_tube_sheath.cxs > format session Opened flip_base.mrc as #9, grid size 512,512,512, pixel 1.39, shown at level 0.272, step 1, values float32 Log from Wed Nov 27 15:30:54 2024UCSF ChimeraX version: 1.8rc202406102315 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. > open > /Users/aninditosen/Documents/P1/baseplate/main_baseplate/baseplate_1.cxs > format session Opened flip_base.mrc as #9, grid size 512,512,512, pixel 1.39, shown at level 0.272, step 1, values float32 Log from Sun Jul 9 21:19:02 2023UCSF ChimeraX version: 1.6.dev202212092052 (2022-12-09) © 2016-2022 Regents of the University of California. All rights reserved. > open > /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/colo_bp.cxs Opened flip_base.mrc as #9, grid size 512,512,512, pixel 1.39, shown at level 0.272, step 1, values float32 Log from Sun Jul 9 13:23:10 2023UCSF ChimeraX version: 1.6.dev202212092052 (2022-12-09) © 2016-2022 Regents of the University of California. All rights reserved. > open > /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/colo_bp2.cxs Opened flip_base.mrc as #9, grid size 512,512,512, pixel 1.39, shown at level 0.272, step 1, values float32 Log from Sat Jul 8 00:54:29 2023UCSF ChimeraX version: 1.6.dev202212092052 (2022-12-09) © 2016-2022 Regents of the University of California. All rights reserved. > open > /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/colo_bp.cxs Opened flip_base.mrc as #9, grid size 512,512,512, pixel 1.39, shown at level 0.272, step 1, values float32 Log from Sat Jul 8 00:43:50 2023UCSF ChimeraX version: 1.6.dev202212092052 (2022-12-09) © 2016-2022 Regents of the University of California. All rights reserved. > open > /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/colo_bp.cxs Opened flip_base.mrc as #9, grid size 512,512,512, pixel 1.39, shown at level 0.272, step 1, values float32 Log from Sat Jul 8 00:09:27 2023UCSF ChimeraX version: 1.6.dev202212092052 (2022-12-09) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/UpfC_af.pdb Chain information for UpfC_af.pdb #1 --- Chain | Description 9 | No description available > open > /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/BplAminus.pdb > /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/BplAplus.pdb > /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/BplB_rings.cif > /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/PmgA.pdb > /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/PmgG.pdb > /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/Tub.pdb > /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/UpfC_af.pdb > /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/flip_base.mrc > /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/gp5_af.pdb > /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/gp6_af.pdb > /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/gp16.pdb > /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/gp22_lastring.pdb > /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/gp22_onebeforelastring.pdb > /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/gp22_theotherrings.cif > /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/gp26.pdb Summary of feedback from opening /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/BplB_rings.cif --- warnings | Missing entity information. Treating each chain as a separate entity. Atom H is not in the residue template for MET /BA:204 Atom 1HA is not in the residue template for GLY /BA:205 Atom 1HB is not in the residue template for HIS /BA:206 Atom 1HB is not in the residue template for ASN /BA:207 Atom 1HB is not in the residue template for ASN /BA:208 Atom 1HG2 is not in the residue template for THR /BA:209 Atom 1HB is not in the residue template for LYS /BA:210 Atom 1HA is not in the residue template for GLY /BA:211 Atom 1HB is not in the residue template for ASN /BA:212 Too many hydrogens missing from residue template(s) to warn about Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. Summary of feedback from opening /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/gp22_theotherrings.cif --- warnings | Missing entity information. Treating each chain as a separate entity. Atom H is not in the residue template for MET /AA:1 Atom 1HB is not in the residue template for SER /AA:2 Atom 1HB is not in the residue template for GLN /AA:3 Atom 1HB is not in the residue template for TYR /AA:4 Atom 1HB is not in the residue template for SER /AA:5 Atom 1HG1 is not in the residue template for ILE /AA:6 Atom 1HB is not in the residue template for GLN /AA:7 Atom 1HB is not in the residue template for GLN /AA:8 Atom 1HB is not in the residue template for SER /AA:9 Too many hydrogens missing from residue template(s) to warn about Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. Chain information for BplAminus.pdb #2 --- Chain | Description Y Z a b c d | No description available Chain information for BplAplus.pdb #3 --- Chain | Description e f g h i j | No description available Chain information for BplB_rings.cif #4 --- Chain | Description BA BB BC BD BE BF BG BH BJ BK BL BN BP BQ BR BS BT BU BV BW BY Bb Bc Bd | No description available Chain information for PmgA.pdb #5 --- Chain | Description M N O P Q R | No description available Chain information for PmgG.pdb #6 --- Chain | Description G H I J K L | No description available Chain information for Tub.pdb #7 --- Chain | Description A B C D E F | No description available Chain information for UpfC_af.pdb #8 --- Chain | Description 9 | No description available Opened flip_base.mrc as #9, grid size 512,512,512, pixel 1.39, shown at level 0.162, step 2, values float32 Chain information for gp5_af.pdb #10 --- Chain | Description 6 7 8 | No description available Chain information for gp6_af.pdb #11 --- Chain | Description 3 4 5 | No description available Chain information for gp16.pdb #12 --- Chain | Description k l m n o p | No description available Chain information for gp22_lastring.pdb #13 --- Chain | Description q r s t u v | No description available Chain information for gp22_onebeforelastring.pdb #14 --- Chain | Description 1 2 w x y z | No description available Chain information for gp22_theotherrings.cif #15 --- Chain | Description AA AB AC AD AE AF AG AH AI AJ AL AM AN AO AP AQ AS AT AV AW AZ Aa Ab Ad | No description available Chain information for gp26.pdb #16 --- Chain | Description S T U V W X | No description available > set bgColor white > transparency 50 > show cartoons > hide atoms > volume #9 level 0.12 > volume #9 level 0.2 > volume #9 step 1 > volume #9 level 272 > volume #9 level 0.272 > set bgColor black > set bgColor white > hide #!9 models > save > /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/baseplate.cxs > hide #14 models > hide #15 models > hide #13 models > select add #1 1316 atoms, 1328 bonds, 94 residues, 1 model selected > ui tool show ""Color Actions"" > color sel salmon > color sel magenta > color sel purple > select subtract #1 Nothing selected > color violet > select add #1 1316 atoms, 1328 bonds, 94 residues, 1 model selected > color sel violet [Repeated 1 time(s)] > color sel medium orchid > color sel dark violet > color sel medium purple > color sel blue violet > color sel dark violet > select subtract #1 Nothing selected > select add #2 44988 atoms, 45492 bonds, 2862 residues, 1 model selected > color sel yellow > color sel gold > color sel yellow > color sel gold > color sel orange > color sel gold > select subtract #2 Nothing selected > select add #3 44988 atoms, 45492 bonds, 2862 residues, 1 model selected > color sel orange > select add #2 89976 atoms, 90984 bonds, 5724 residues, 2 models selected > select subtract #3 44988 atoms, 45492 bonds, 2862 residues, 1 model selected QDockWidget failed to find relevant screen info. screenFrom: QScreen(0x1527960, name=""eDP-1"") screenTo: QScreen(0x1527960, name=""eDP-1"") wdgScreen: QScreen(0x1527960, name=""eDP-1"") orgWdgScreen QScreen(0x0) [Repeated 25 time(s)] > select clear > select add #4 62808 atoms, 63336 bonds, 4056 residues, 1 model selected > color sel peru > select clear > select add #4 62808 atoms, 63336 bonds, 4056 residues, 1 model selected > color sel peach puff > color sel wheat > color sel burly wood > select clear > select add #5 11142 atoms, 11256 bonds, 708 residues, 1 model selected > ui tool show ""Color Actions"" > color sel turquoise > select subtract #5 Nothing selected > select add #5 11142 atoms, 11256 bonds, 708 residues, 1 model selected > color sel medium aquamarine > color sel dodger blue > color sel dark turquoise > color sel medium sea green > color sel cornflower blue > color sel sea green > color sel spring green > color sel dark turquoise > color sel medium spring green > color sel dark cyan > color sel steel blue > color sel medium aquamarine > color sel dark cyan > color sel cornflower blue > color sel medium turquoise > color sel light sea green > color sel dodger blue > color sel medium spring green > color sel dark turquoise > color sel dark cyan > color sel light sea green > color sel teal > color sel steel blue > color sel cadet blue > color sel green > color sel light slate gray > color sel deep sky blue > color sel dark turquoise > color sel medium spring green > color sel medium turquoise > color sel light sea green > color sel dark cyan > select subtract #5 Nothing selected > select add #6 17226 atoms, 17406 bonds, 1158 residues, 1 model selected > color sel green > color sel forest green > select clear > color medium spring green > select add #1 1316 atoms, 1328 bonds, 94 residues, 1 model selected > ui tool show ""Color Actions"" > color sel dark magenta > color sel dark violet > select subtract #1 Nothing selected > select add #1 1316 atoms, 1328 bonds, 94 residues, 1 model selected > color sel dark orchid > select add #2 46304 atoms, 46820 bonds, 2956 residues, 2 models selected > select subtract #1 44988 atoms, 45492 bonds, 2862 residues, 1 model selected > color sel dark orchid [Repeated 1 time(s)] > select subtract #2 Nothing selected > select add #1 1316 atoms, 1328 bonds, 94 residues, 1 model selected > color sel dark magenta > select subtract #1 Nothing selected > select add #1 1316 atoms, 1328 bonds, 94 residues, 1 model selected > color sel purple > select add #2 46304 atoms, 46820 bonds, 2956 residues, 2 models selected > select subtract #1 44988 atoms, 45492 bonds, 2862 residues, 1 model selected > select subtract #2 Nothing selected > select add #1 1316 atoms, 1328 bonds, 94 residues, 1 model selected > color sel dark violet > color sel dark orchid > color sel dark magenta > select subtract #1 Nothing selected > select add #2 44988 atoms, 45492 bonds, 2862 residues, 1 model selected > color sel orange > color sel gold > select subtract #2 Nothing selected > select add #3 44988 atoms, 45492 bonds, 2862 residues, 1 model selected > color sel dark orange > color sel orange > select subtract #3 Nothing selected > select add #4 62808 atoms, 63336 bonds, 4056 residues, 1 model selected QDockWidget failed to find relevant screen info. screenFrom: QScreen(0x1527960, name=""eDP-1"") screenTo: QScreen(0x1527960, name=""eDP-1"") wdgScreen: QScreen(0x1527960, name=""eDP-1"") orgWdgScreen QScreen(0x0) [Repeated 26 time(s)] > color sel light salmon > color sel burly wood > select subtract #4 Nothing selected > select add #5 11142 atoms, 11256 bonds, 708 residues, 1 model selected > color sel dark turquoise > select subtract #5 Nothing selected > select add #6 17226 atoms, 17406 bonds, 1158 residues, 1 model selected > color sel green > color sel lawn green > select subtract #6 Nothing selected > select add #6 17226 atoms, 17406 bonds, 1158 residues, 1 model selected > color sel green > color sel lime green > color sel forest green > color sel lime green > select subtract #6 Nothing selected > select add #7 16794 atoms, 16968 bonds, 1080 residues, 1 model selected > color sel salmon > select subtract #7 Nothing selected > select add #8 1316 atoms, 1328 bonds, 94 residues, 1 model selected > color sel dark slate blue [Repeated 2 time(s)] > select subtract #8 Nothing selected > select add #10 9078 atoms, 9180 bonds, 630 residues, 1 model selected > ui tool show ""Color Actions"" > color sel magenta > color sel dark orchid > color sel medium purple > color sel dark orchid > select subtract #10 Nothing selected > save > /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/colo_bp.cxs > select add #11 15663 atoms, 15825 bonds, 1014 residues, 1 model selected > color sel orchid [Repeated 1 time(s)] > color sel dark violet > color sel slate blue > color sel blue violet > select subtract #11 Nothing selected > select add #11 15663 atoms, 15825 bonds, 1014 residues, 1 model selected > color sel dark violet > color sel dark orchid > color sel medium purple > color sel dark orchid > color sel slate blue > color sel dark slate blue > color sel purple > color sel dark orchid > color sel dark blue > color sel cornflower blue > color sel dodger blue > color sel medium slate blue > color sel slate blue > color sel blue violet > select subtract #11 Nothing selected > select add #12 26394 atoms, 26664 bonds, 1668 residues, 1 model selected > color sel goldenrod > select subtract #12 Nothing selected > select add #12 26394 atoms, 26664 bonds, 1668 residues, 1 model selected > color sel dark khaki > select subtract #12 Nothing selected > select add #13 47784 atoms, 48270 bonds, 3174 residues, 1 model selected > color sel light steel blue > select subtract #13 Nothing selected > select add #14 47784 atoms, 48270 bonds, 3174 residues, 1 model selected > color sel wheat > select add #15 238920 atoms, 241350 bonds, 15870 residues, 2 models selected > select subtract #14 191136 atoms, 193080 bonds, 12696 residues, 1 model selected > color sel plum > select add #16 203346 atoms, 205410 bonds, 13446 residues, 2 models selected > color sel dark sea green QDockWidget failed to find relevant screen info. screenFrom: QScreen(0x1527960, name=""eDP-1"") screenTo: QScreen(0x1527960, name=""eDP-1"") wdgScreen: QScreen(0x1527960, name=""eDP-1"") orgWdgScreen QScreen(0x0) [Repeated 67 time(s)] > select subtract #15 12210 atoms, 12330 bonds, 750 residues, 1 model selected > select subtract #16 Nothing selected > save > /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/colo_bp.cxs > select add #10 9078 atoms, 9180 bonds, 630 residues, 1 model selected > select subtract #10 Nothing selected > select add #11 15663 atoms, 15825 bonds, 1014 residues, 1 model selected > ui tool show ""Color Actions"" > color sel dark orchid > color sel dark magenta > color sel slate blue > color sel dark slate blue > color sel magenta > color sel blue violet > save > /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/colo_bp.cxs ——— End of log from Sat Jul 8 00:09:27 2023 ——— opened ChimeraX session > select add #1 16979 atoms, 17153 bonds, 1108 residues, 2 models selected > ui tool show ""Color Actions"" > color sel magenta > color sel hot pink > color sel medium violet red > select subtract #1 15663 atoms, 15825 bonds, 1014 residues, 1 model selected > select add #1 16979 atoms, 17153 bonds, 1108 residues, 2 models selected > color sel deep pink > color sel purple > color sel medium violet red > select subtract #1 15663 atoms, 15825 bonds, 1014 residues, 1 model selected > save > /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/colo_bp.cxs ——— End of log from Sat Jul 8 00:43:50 2023 ——— opened ChimeraX session > show sel atoms > hide sel atoms > ui tool show ""Color Actions"" > color sel slate blue > color sel blue violet > color sel dark orchid > color sel blue violet > color sel royal blue > color sel indigo > color sel dark blue > color sel medium blue > color sel cornflower blue > color sel midnight blue > color sel dark slate blue > color sel medium slate blue > color sel dark blue > color sel navy > color sel indigo > color sel steel blue > color sel navy > color sel indigo > color sel slate blue > color sel medium slate blue > color sel blue violet > color sel dark violet [Repeated 1 time(s)] > color sel blue violet > color sel slate blue > select subtract #11 Nothing selected > show #1-8,10-12,16 atoms > hide #1-8,10-12,16 cartoons > select add #16 12210 atoms, 12330 bonds, 750 residues, 1 model selected > select subtract #16 Nothing selected > select add #16 12210 atoms, 12330 bonds, 750 residues, 1 model selected > select subtract #16 Nothing selected > select add #11 15663 atoms, 15825 bonds, 1014 residues, 1 model selected > select subtract #11 Nothing selected > select add #10 9078 atoms, 9180 bonds, 630 residues, 1 model selected > style sel sphere Changed 9078 atom styles > hide sel cartoons > select add #1 10394 atoms, 10508 bonds, 724 residues, 2 models selected > style sel sphere Changed 10394 atom styles > select subtract #1 9078 atoms, 9180 bonds, 630 residues, 1 model selected > select subtract #10 Nothing selected > lighting soft > select add #9 2 models selected > select subtract #9 Nothing selected > select add #5 11142 atoms, 11256 bonds, 708 residues, 1 model selected > ui tool show ""Color Actions"" > color sel light sea green > color sel dark cyan > select subtract #5 Nothing selected > save > /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/colo_bp2.cxs ——— End of log from Sat Jul 8 00:54:29 2023 ——— opened ChimeraX session > hide #1-8,10-12,16 atoms > show #1-8,10-12,16 cartoons > lighting soft > lighting full > lighting shadows false > lighting shadows true > graphics silhouettes true > lighting flat > graphics silhouettes false > graphics silhouettes true > lighting flat > lighting full > lighting soft > graphics silhouettes false > lighting soft > lighting full > lighting shadows false > lighting shadows true > lighting simple > graphics silhouettes true > lighting full > lighting soft > save > /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/colo_bp.cxs ——— End of log from Sun Jul 9 13:23:10 2023 ——— opened ChimeraX session > hide #2 models > hide #4 models > hide #3 models > hide #5 models > hide #6 models > show #6 models > hide #12 models > hide #11 models > show #11 models > hide #10 models > show #10 models > hide #16 models > hide #8 models > save /home/andy/Desktop/image9.png supersample 3 > show #4 models > hide #4 models > show #16 models > hide #16 models > show #5 models > save /home/andy/Desktop/image10.png supersample 3 > save /home/andy/Desktop/image11.png supersample 3 > turn x 90 [Repeated 2 time(s)] > hide #10 models > show #10 models > hide #11 models > show #11 models > hide #10 models > show #10 models > hide #5 models > show #5 models > hide #5 models > turn x -90 > save /home/andy/Desktop/image9.png supersample 3 > turn x 90 > save /home/andy/Desktop/image10.png supersample 3 > show #5 models > save /home/andy/Desktop/image11.png supersample 3 > turn x -90 > save /home/andy/Desktop/image12.png supersample 3 > turn x 90 > show #12 models > hide #12 models > show #16 models > save /home/andy/Desktop/image13.png supersample 3 > turn x -90 > save /home/andy/Desktop/image14.png supersample 3 > turn x 90 > show #12 models > save /home/andy/Desktop/image15.png supersample 3 > turn x -90 > save /home/andy/Desktop/image16.png supersample 3 > turn x 90 > show #2 models > save /home/andy/Desktop/image17.png supersample 3 > turn x -90 > save /home/andy/Desktop/image18.png supersample 3 > turn x 90 > show #3 models > save /home/andy/Desktop/image19.png supersample 3 > turn x -90 > save /home/andy/Desktop/image20.png supersample 3 > turn x 90 > show #4 models > save /home/andy/Desktop/image21.png supersample 3 > hide #4 models > save > /home/andy/Documents/P1/baseplate/realspace_refined_025_namecorrect/baseplate.cxs ——— End of log from Sun Jul 9 21:19:02 2023 ——— opened ChimeraX session > color #2 #ffd70011 > color #2 #ffd70012 > color #3 #ffa50011 > color #3 #ffa50012 > color #12 #bdb76b14 > select add #16 12210 atoms, 12330 bonds, 750 residues, 1 model selected > select add #6 29436 atoms, 29736 bonds, 1908 residues, 2 models selected > select subtract #6 12210 atoms, 12330 bonds, 750 residues, 1 model selected > select add #5 23352 atoms, 23586 bonds, 1458 residues, 2 models selected > show sel surfaces > lighting simple > lighting full > sel: #5/Q Unknown command: sel: #5/Q > transparency sel 50 > show sel surfaces > transparency sel 0 > select clear > sel: #5/Q Unknown command: sel: #5/Q > select #5/Q 1857 atoms, 1876 bonds, 118 residues, 1 model selected > transparency sel 50 > select #16/V 2035 atoms, 2055 bonds, 125 residues, 1 model selected > transparency sel 50 > select #16/V 2035 atoms, 2055 bonds, 125 residues, 1 model selected > hide sel cartoons > show sel surfaces > transparency sel 0 > select #5/Q 1857 atoms, 1876 bonds, 118 residues, 1 model selected > transparency sel 0 > select #16/X 2035 atoms, 2055 bonds, 125 residues, 1 model selected > surface hidePatches (#!16 & sel) > save /Users/aninditosen/Documents/P1/baseplate/full_fig.cxs > hide (#!16 & sel) target a > delete atoms (#!16 & sel) > delete bonds (#!16 & sel) > color #2 gold > color #3 orange > select add #2 44988 atoms, 45492 bonds, 2862 residues, 1 model selected > select add #3 89976 atoms, 90984 bonds, 5724 residues, 2 models selected > select add #12 116370 atoms, 117648 bonds, 7392 residues, 3 models selected > show sel cartoons > show sel surfaces > select subtract #12 89976 atoms, 90984 bonds, 5724 residues, 20 models selected > select subtract #3 44988 atoms, 45492 bonds, 2862 residues, 13 models selected > color #2 gold > color #2 #ffd700d3 > color #2 gold > color #2 #ffd70021 > color #2 gold > hide sel surfaces > select subtract #2 6 models selected > select add #3 44988 atoms, 45492 bonds, 2862 residues, 1 model selected > color #3 orange > hide sel surfaces > color #12 darkkhaki > hide sel surfaces > select add #12 71382 atoms, 72156 bonds, 4530 residues, 8 models selected > hide sel surfaces > select clear > select #2/d 7498 atoms, 7582 bonds, 477 residues, 1 model selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > select #12/p 4399 atoms, 4444 bonds, 278 residues, 1 model selected > delete atoms (#!12 & sel) > delete bonds (#!12 & sel) > select #3/j 7498 atoms, 7582 bonds, 477 residues, 1 model selected > delete atoms (#!3 & sel) > delete bonds (#!3 & sel) > save > /Users/aninditosen/Documents/P1/baseplate/main_baseplate/all_baseplate_tube_sheath.cxs > select #5/P 1857 atoms, 1876 bonds, 118 residues, 1 model selected > surface hidePatches (#!5 & sel) > delete atoms (#!5 & sel) > delete bonds (#!5 & sel) > select #2/c 7498 atoms, 7582 bonds, 477 residues, 1 model selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > show #4 models > show #13 models > save > /Users/aninditosen/Documents/P1/baseplate/main_baseplate/all_baseplate_tube_sheath.cxs ——— End of log from Wed Nov 27 15:30:54 2024 ——— opened ChimeraX session > show #1,4,6-7,10-11,13#!2-3,5,12,16 surfaces > select add #7 16794 atoms, 16968 bonds, 1080 residues, 1 model selected > select add #4 79602 atoms, 80304 bonds, 5136 residues, 8 models selected > hide sel cartoons > transparency sel 50 > color #7 #fa807236 > color #4 #b2b2b235 > color #4 #b2b2b236 > select subtract #7 62808 atoms, 63336 bonds, 4056 residues, 31 models selected > select subtract #4 24 models selected > graphics silhouettes false > select #13/u :1-100 1463 atoms, 1478 bonds, 100 residues, 1 model selected > ui tool show ""Color Actions"" > color sel dark turquoise > select #13/u :101-240 2103 atoms, 2119 bonds, 140 residues, 1 model selected > color sel salmon > select #13/u :241-400 2401 atoms, 2428 bonds, 160 residues, 1 model selected > color sel cornflower blue > select #13/u :401-530 1997 atoms, 2017 bonds, 129 residues, 1 model selected > color sel fire brick > select add #13 47784 atoms, 48270 bonds, 3174 residues, 2 models selected > select subtract #13 6 models selected > cd /Users/aninditosen/Documents/P1/baseplate/main_baseplate Current working directory is: /Users/aninditosen/Documents/P1/baseplate/main_baseplate > save > /Users/aninditosen/Documents/P1/baseplate/main_baseplate/all_baseplate_tube_sheath4.cxs ——— End of log from Mon Dec 2 16:19:56 2024 ——— opened ChimeraX session > color #1 #c715850a > color #1 #c715853d > color #1 #c7158516 > color #1 #c715850b > color #2 #ffd7000c > hide #!2 models > color #2 #ffd7000d > show #!2 models > color #2 #ffd700fb > hide #!2 models > show #!2 models > color #2 #ffd70021 > color #2 #ffd700fd > hide #2.1 models > show #2.1 models > hide #2.2 models > show #2.2 models > hide #2.3 models > show #2.3 models > select add #2.3 7498 atoms, 477 residues, 1 model selected > select add #2 29992 atoms, 30328 bonds, 1908 residues, 2 models selected > select subtract #2 4 models selected > color #2 #ffd70013 > color #2 #ffd70014 > color #2.3 #ffd700fd > color #2.3 #ffd700fc > color #12 #bdb76b08 > color #12 darkkhaki > select add #12.5 4399 atoms, 278 residues, 1 model selected > select subtract #12.5 1 model selected > select add #12.4 4399 atoms, 278 residues, 1 model selected > select subtract #12.4 1 model selected > select add #12.3 4399 atoms, 278 residues, 1 model selected > select subtract #12.3 1 model selected > select add #12.2 4399 atoms, 278 residues, 1 model selected > select subtract #12.2 1 model selected > select add #12.3 4399 atoms, 278 residues, 1 model selected > select subtract #12.3 1 model selected > select add #12.3 4399 atoms, 278 residues, 1 model selected > select subtract #12.3 1 model selected > color #12 darkkhaki > color #12 #bdb76b09 > color #12 #bdb76b14 > color #12 #bdb76b2a > color #12 #bdb76b1a > color #12.4 darkkhaki > color #12.4 #bdb76b16 > hide #12.3 models > color #12.4 #bdb76b17 > show #12.3 models > color #12.3 #bdb76bfd > color #12.3 darkkhaki > save > /Users/aninditosen/Documents/P1/baseplate/main_baseplate/full_baseplate.cxs ——— End of log from Mon Dec 2 17:54:21 2024 ——— opened ChimeraX session > show #!1-7,10-13,16 cartoons > hide #!1-7,10-13,16 surfaces > color #1 mediumvioletred > select add #1 1316 atoms, 1328 bonds, 94 residues, 1 model selected > color #1 mediumvioletred > select subtract #1 1 model selected > select add #1 1316 atoms, 1328 bonds, 94 residues, 1 model selected > show sel cartoons [Repeated 1 time(s)] > transparency sel 50 > transparency sel 0 > color #1 #c7158500 > color #1 #c715857c > color #1 #c71585fc > select subtract #1 1 model selected > color #12 darkkhaki > color #2 gold > color #3 #ffa500f7 > lighting soft > lighting full > graphics silhouettes true > ui tool show ""Side View"" > save /Users/aninditosen/Documents/P1/baseplate/main_baseplate/all_base2.cxs > lighting full > lighting soft > lighting full > lighting flat [Repeated 1 time(s)] > graphics silhouettes false > graphics silhouettes true > lighting full > color #7 salmon [Repeated 1 time(s)] > color #7 #fa8072aa > color #7 #fa80727b > color #7 #fa807260 > color #7 #fa807280 > save /Users/aninditosen/Desktop/image9.png supersample 3 > hide #!16 models > hide #!2 models > hide #!3 models > hide #!7 models > hide #!6 models > hide #!11 models > hide #!12 models > ui windowfill toggle [Repeated 1 time(s)] > select add #5 9285 atoms, 9380 bonds, 590 residues, 1 model selected > show sel surfaces > select #13/t 7964 atoms, 8045 bonds, 529 residues, 1 model selected > hide (#!13 & sel) target a > delete atoms (#!13 & sel) > delete bonds (#!13 & sel) > select #5/n 1857 atoms, 1876 bonds, 118 residues, 1 model selected > select #5/N 1857 atoms, 1876 bonds, 118 residues, 1 model selected > hide sel surfaces > hide sel cartoons > hbonds sel reveal true 83 hydrogen bonds found > select clear > ~hbonds > select #13/u #5/O 9821 atoms, 9921 bonds, 647 residues, 2 models selected > hbonds sel reveal true 537 hydrogen bonds found > style sel stick Changed 9821 atom styles > ~hbonds > select clear > hide #!1,4-5,10,13 atoms > show #!12 models > show #!2 models > show #!3 models > lighting full > lighting soft > lighting simple > select #5/M 1857 atoms, 1876 bonds, 118 residues, 1 model selected > hide sel surfaces > select up 9285 atoms, 9380 bonds, 590 residues, 2 models selected > ~hbonds > select clear > ~hbonds [Repeated 1 time(s)] > select 511878 atoms, 517059 bonds, 33539 residues, 26 models selected > ~hbonds > style sel & #!1-5,10,12-13 stick Changed 211784 atom styles > select clear > hide #!2 models > select #13/s 7964 atoms, 8045 bonds, 529 residues, 1 model selected > hide sel cartoons > select #14?BN Expected an objects specifier or a keyword > select #14/BN Nothing selected > select #14/BN Nothing selected > select #4/BN:178 15 atoms, 14 bonds, 1 residue, 1 model selected > select up 55 atoms, 54 bonds, 4 residues, 2 models selected > select up 2617 atoms, 2639 bonds, 169 residues, 2 models selected > select up 62808 atoms, 63336 bonds, 4056 residues, 2 models selected > hide sel cartoons > select #13/v 7964 atoms, 8045 bonds, 529 residues, 1 model selected > hide sel cartoons > select #12/m #3.g Expected a keyword > select #12/m #3/g 11897 atoms, 12026 bonds, 755 residues, 2 models selected > hide sel cartoons > select #12/m #3/f 11897 atoms, 12026 bonds, 755 residues, 2 models selected > hide sel cartoons > select #12/o #13/i 4399 atoms, 4444 bonds, 278 residues, 1 model selected > hide sel cartoons > select #12/o #3/i 11897 atoms, 12026 bonds, 755 residues, 2 models selected > hide sel cartoons > show #!2 models > select #12/o #3/i #2/a 19395 atoms, 19608 bonds, 1232 residues, 3 models selected > hide sel cartoons > select #12/o #3/i #2/Z 19395 atoms, 19608 bonds, 1232 residues, 3 models selected > hide sel cartoons > hide #!10 models > hide sel atoms > select clear > hide #!1-5,12-13 atoms > select add #3 37490 atoms, 37910 bonds, 2385 residues, 1 model selected > select subtract #3 5 models selected > show #!7 models > hide #!7 models > select #13/u :516 #5/O :61 21 atoms, 19 bonds, 2 residues, 2 models selected > hbonds sel reveal true 1 hydrogen bonds found > select clear > select #13/u :522 #5/O :114 34 atoms, 32 bonds, 2 residues, 2 models selected > hbonds sel reveal true 3 hydrogen bonds found > select clear > select #13/u :522 :516 #5/O :114 :61 55 atoms, 51 bonds, 4 residues, 2 models selected > hbonds sel reveal true 4 hydrogen bonds found > hide sel surfaces [Repeated 1 time(s)] > show sel surfaces > hide sel surfaces > select clear > color #17 #00bfff00 models > color #17 deepskyblue models > color #17 #fa0908ff models > color #17 #fa8b87ff models > save /Users/aninditosen/Documents/P1/baseplate/main_baseplate/all_base3.cxs ——— End of log from Wed Dec 4 16:01:10 2024 ——— > view name session-start opened ChimeraX session > ui tool show ""Side View"" > show #!16 models > select add #16 10175 atoms, 10275 bonds, 625 residues, 1 model selected > show sel surfaces > graphics silhouettes false > select add #13 49995 atoms, 50500 bonds, 3270 residues, 7 models selected > show sel surfaces > lighting soft [Repeated 1 time(s)] > lighting full [Repeated 1 time(s)]An error occurred in drawing the scene. Redrawing graphics is now stopped to avoid a continuous stream of error messages. To restart graphics use the command ""graphics restart"" after changing the settings that caused the error. GLError( err = 1285, description = b'out of memory', baseOperation = glTexImage2D, pyArgs = ( GL_TEXTURE_2D, 0, GL_DEPTH_COMPONENT24, 2048, 2048, 0, GL_DEPTH_COMPONENT, GL_FLOAT, c_void_p(None), ), cArgs = ( GL_TEXTURE_2D, 0, GL_DEPTH_COMPONENT24, 2048, 2048, 0, GL_DEPTH_COMPONENT, GL_FLOAT, c_void_p(None), ), cArguments = ( GL_TEXTURE_2D, 0, GL_DEPTH_COMPONENT24, 2048, 2048, 0, GL_DEPTH_COMPONENT, GL_FLOAT, c_void_p(None), ) ) Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.11\bin\Lib\site- packages\chimerax\core\updateloop.py"", line 84, in draw_new_frame view.draw(check_for_changes = False) File ""C:\Program Files\ChimeraX 1.11\bin\Lib\site- packages\chimerax\graphics\view.py"", line 188, in draw self._draw_scene(camera, drawings) File ""C:\Program Files\ChimeraX 1.11\bin\Lib\site- packages\chimerax\graphics\view.py"", line 227, in _draw_scene shadow, multishadow = self._compute_shadowmaps(opaque_drawings, transparent_drawings, camera) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.11\bin\Lib\site- packages\chimerax\graphics\view.py"", line 631, in _compute_shadowmaps shadow_enabled = r.shadow.use_shadow_map(camera, shadow_drawings) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.11\bin\Lib\site- packages\chimerax\graphics\opengl.py"", line 1551, in use_shadow_map self._start_rendering_shadowmap(center, radius, size) File ""C:\Program Files\ChimeraX 1.11\bin\Lib\site- packages\chimerax\graphics\opengl.py"", line 1583, in _start_rendering_shadowmap fb = r.start_depth_render(self._shadow_map_framebuffer, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.11\bin\Lib\site- packages\chimerax\graphics\opengl.py"", line 1372, in start_depth_render dt.initialize_depth((size, size)) File ""C:\Program Files\ChimeraX 1.11\bin\Lib\site- packages\chimerax\graphics\opengl.py"", line 3071, in initialize_depth self.initialize_texture(size, format, iformat, tdtype, ncomp, File ""C:\Program Files\ChimeraX 1.11\bin\Lib\site- packages\chimerax\graphics\opengl.py"", line 3097, in initialize_texture GL.glTexImage2D(gl_target, 0, iformat, size[0], size[1], 0, format, File ""src/latebind.pyx"", line 40, in OpenGL_accelerate.latebind.LateBind.__call__ File ""src/wrapper.pyx"", line 319, in OpenGL_accelerate.wrapper.Wrapper.__call__ File ""src/wrapper.pyx"", line 312, in OpenGL_accelerate.wrapper.Wrapper.__call__ File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1285, description = b'out of memory', baseOperation = glTexImage2D, pyArgs = ( GL_TEXTURE_2D, 0, GL_DEPTH_COMPONENT24, 2048, 2048, 0, GL_DEPTH_COMPONENT, GL_FLOAT, c_void_p(None), ), cArgs = ( GL_TEXTURE_2D, 0, GL_DEPTH_COMPONENT24, 2048, 2048, 0, GL_DEPTH_COMPONENT, GL_FLOAT, c_void_p(None), ), cArguments = ( GL_TEXTURE_2D, 0, GL_DEPTH_COMPONENT24, 2048, 2048, 0, GL_DEPTH_COMPONENT, GL_FLOAT, c_void_p(None), ) ) Exception ignored in: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.11\bin\Lib\site- packages\chimerax\graphics\opengl.py"", line 3165, in __del__ raise OpenGLError('OpenGL texture was not deleted before graphics.Texture destroyed') chimerax.graphics.opengl.OpenGLError: OpenGL texture was not deleted before graphics.Texture destroyed > lighting soft > lighting simple > lighting soft > lighting full > select add #13 49995 atoms, 50500 bonds, 3270 residues, 15 models selected Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.11\bin\Lib\site- packages\chimerax\model_panel\tool.py"", line 480, in _tree_change_cb run(self.session, ""select "" + mode + "" #"" + model.id_string) File ""C:\Program Files\ChimeraX 1.11\bin\Lib\site- packages\chimerax\core\commands\run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.11\bin\Lib\site- packages\chimerax\core\commands\cli.py"", line 3237, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.11\bin\Lib\site- packages\chimerax\std_commands\select.py"", line 120, in select_add report_selection(session) File ""C:\Program Files\ChimeraX 1.11\bin\Lib\site- packages\chimerax\std_commands\select.py"", line 192, in report_selection session.logger.status(', '.join(lines) + ' selected', log = True) File ""C:\Program Files\ChimeraX 1.11\bin\Lib\site- packages\chimerax\core\logger.py"", line 522, in status StatusLogger.status(self, msg, **kw) File ""C:\Program Files\ChimeraX 1.11\bin\Lib\site- packages\chimerax\core\logger.py"", line 220, in status if l.status(msg, color, secondary) and getattr( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.11\bin\Lib\site- packages\chimerax\ui\gui.py"", line 1133, in status sbar.status(msg, color, secondary) File ""C:\Program Files\ChimeraX 1.11\bin\Lib\site- packages\chimerax\ui\statusbar.py"", line 165, in status self._draw_text(msg, color, secondary) File ""C:\Program Files\ChimeraX 1.11\bin\Lib\site- packages\chimerax\ui\statusbar.py"", line 175, in _draw_text draw_overlays(dlist, self._renderer) File ""C:\Program Files\ChimeraX 1.11\bin\Lib\site- packages\chimerax\graphics\drawing.py"", line 1613, in draw_overlays _draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS) File ""C:\Program Files\ChimeraX 1.11\bin\Lib\site- packages\chimerax\graphics\drawing.py"", line 1572, in _draw_multiple d.draw(renderer, draw_pass) File ""C:\Program Files\ChimeraX 1.11\bin\Lib\site- packages\chimerax\graphics\drawing.py"", line 784, in draw self.draw_self(renderer, draw_pass) File ""C:\Program Files\ChimeraX 1.11\bin\Lib\site- packages\chimerax\graphics\drawing.py"", line 795, in draw_self self._draw_geometry(renderer, transparent_only = any_opaque) File ""C:\Program Files\ChimeraX 1.11\bin\Lib\site- packages\chimerax\graphics\drawing.py"", line 831, in _draw_geometry t.bind_texture() File ""C:\Program Files\ChimeraX 1.11\bin\Lib\site- packages\chimerax\graphics\opengl.py"", line 3177, in bind_texture self.fill_opengl_texture() File ""C:\Program Files\ChimeraX 1.11\bin\Lib\site- packages\chimerax\graphics\opengl.py"", line 3220, in fill_opengl_texture self.initialize_texture(size, format, iformat, tdtype, ncomp, data) File ""C:\Program Files\ChimeraX 1.11\bin\Lib\site- packages\chimerax\graphics\opengl.py"", line 3097, in initialize_texture GL.glTexImage2D(gl_target, 0, iformat, size[0], size[1], 0, format, File ""src/latebind.pyx"", line 40, in OpenGL_accelerate.latebind.LateBind.__call__ File ""src/wrapper.pyx"", line 319, in OpenGL_accelerate.wrapper.Wrapper.__call__ File ""src/wrapper.pyx"", line 312, in OpenGL_accelerate.wrapper.Wrapper.__call__ File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1285, description = b'out of memory', baseOperation = glTexImage2D, pyArgs = ( GL_TEXTURE_2D, 0, GL_RGBA8, 811, 46, 0, GL_RGBA, GL_UNSIGNED_BYTE, array([[[0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0], ..., [0, 0, 0, 0], [0, 0, 0..., ), cArgs = ( GL_TEXTURE_2D, 0, GL_RGBA8, 811, 46, 0, GL_RGBA, GL_UNSIGNED_BYTE, array([[[0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0], ..., [0, 0, 0, 0], [0, 0, 0..., ), cArguments = ( GL_TEXTURE_2D, 0, GL_RGBA8, 811, 46, 0, GL_RGBA, GL_UNSIGNED_BYTE, array([[[0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0], ..., [0, 0, 0, 0], [0, 0, 0..., ) ) OpenGL.error.GLError: GLError( err = 1285, description = b'out of memory', baseOperation = glTexImage2D, pyArgs = ( GL_TEXTURE_2D, 0, GL_RGBA8, 811, 46, 0, GL_RGBA, GL_UNSIGNED_BYTE, array([[[0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0], ..., [0, 0, 0, 0], [0, 0, 0..., ), cArgs = ( GL_TEXTURE_2D, 0, GL_RGBA8, 811, 46, 0, GL_RGBA, GL_UNSIGNED_BYTE, array([[[0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0], ..., [0, 0, 0, 0], [0, 0, 0..., ), cArguments = ( GL_TEXTURE_2D, 0, GL_RGBA8, 811, 46, 0, GL_RGBA, GL_UNSIGNED_BYTE, array([[[0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0], ..., [0, 0, 0, 0], [0, 0, 0..., ) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. OpenGL version: 4.6 (Core Profile) Mesa 26.1.0-devel (git-219807d38d) OpenGL renderer: D3D12 (Qualcomm(R) Adreno(TM) X1-45 GPU) OpenGL vendor: Microsoft Corporation Python: 3.11.9 Locale: en_US.cp1252 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: windows Manufacturer: Microsoft Corporation Model: Surface Pro 12in 1st Ed with Snapdragon OS: Microsoft Windows 11 Home (Build 26200) Memory: 16,756,944,896 MaxProcessMemory: 137,438,953,344 CPU: 8 Snapdragon X Plus (8-core) @ 3.30 GHz OSLanguage: en-US Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.0 appdirs: 1.4.4 asttokens: 3.0.1 attrs: 25.4.0 babel: 2.17.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 3.12.2 build: 1.3.0 certifi: 2025.11.12 cftime: 1.6.5 charset-normalizer: 3.4.4 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.1.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.61.4 ChimeraX-AtomicLibrary: 14.2.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.0 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.11 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.7.3 ChimeraX-Label: 1.2 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.2 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.1.0 ChimeraX-MDcrds: 2.17.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0.1 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.15.2 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.11 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.4.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.5 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.10 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.3 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.49.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.5.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.3.1 colorama: 0.4.6 comm: 0.2.3 comtypes: 1.4.11 contourpy: 1.3.3 coverage: 7.13.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.4 debugpy: 1.8.19 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.61.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.15.1 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.11 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.3.0 ipykernel: 6.30.1 ipython: 9.5.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.8 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.25.1 jsonschema-specifications: 2025.9.1 jupyter_client: 8.6.3 jupyter_core: 5.9.1 jupyterlab_widgets: 3.0.16 kiwisolver: 1.4.9 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.1 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.0 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 1.26.4 nvidia-nvjitlink-cu12: 12.9.86 OpenMM: 8.2.0 OpenMM-CUDA-12: 8.2.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.5 pep517: 0.13.1 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.5.1 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.12.5 pydantic-settings: 2.12.0 pydantic_core: 2.41.5 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.6 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.2.5 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.9.1 PyQt6-Qt6: 6.9.2 PyQt6-WebEngine-commercial: 6.9.0 PyQt6-WebEngine-Qt6: 6.9.2 PyQt6_sip: 13.10.2 pytest: 9.0.2 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.1 python-multipart: 0.0.21 pytz: 2025.2 pywin32: 311 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.0.0 roman-numerals-py: 4.0.0 rpds-py: 0.30.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.2.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 sse-starlette: 3.0.4 stack-data: 0.6.3 starlette: 0.50.0 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.4 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 tzdata: 2025.3 urllib3: 2.6.2 uvicorn: 0.38.0 wcwidth: 0.2.14 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 WMI: 1.5.1 yarl: 1.22.0 }}} " defect closed normal Graphics limitation all ChimeraX