id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5750 Out of space writing file history venkatareddy@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Linux-5.11.0-41-generic-x86_64-with-glibc2.31 ChimeraX Version: 1.3rc202111230539 (2021-11-23 05:39:18 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.3rc202111230539 (2021-11-23) © 2016-2021 Regents of the University of California. All rights reserved. > open 6nj9_interactions.cxs Log from Wed Dec 8 23:04:13 2021UCSF ChimeraX version: 1.3rc202111230539 (2021-11-23) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 6nj9 6nj9 title: Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 2-to-1 complex [more info...] Chain information for 6nj9 #1 --- Chain | Description | UniProt A E | Histone H3.2 | H32_XENLA B F | Histone H4 | H4_XENLA C G | Histone H2A type 1 | H2A1_XENLA D H | Histone H2B 1.1 | H2B11_XENLA I | 601 DNA Strand 1 | J | 601 DNA Strand 2 | K M | Histone-lysine N-methyltransferase, H3 lysine-79 specific | DOT1L_HUMAN L N | Ubiquitin | UBB_HUMAN Non-standard residues in 6nj9 #1 --- SAM — S-adenosylmethionine > show cartoons > hide atoms > select :sam 54 atoms, 58 bonds, 2 residues, 1 model selected > show sel atoms > select clear > select /K:196 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 198 atoms, 205 bonds, 22 residues, 1 model selected > select up 2707 atoms, 2779 bonds, 330 residues, 1 model selected > rainbow sel > select clear > select /K:282 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select /K:305 14 atoms, 15 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select /K:131 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > select /K:243 11 atoms, 11 bonds, 1 residue, 1 model selected > select up 32 atoms, 32 bonds, 4 residues, 1 model selected > show sel atoms > style sel stick Changed 32 atom styles > color sel byhetero > select clear > select /K:500@CE 1 atom, 1 residue, 1 model selected > select up 27 atoms, 29 bonds, 1 residue, 1 model selected > style sel ball Changed 27 atom styles > select clear > select /K:500@CE 1 atom, 1 residue, 1 model selected > cofr sel > select /K:190 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 198 atoms, 205 bonds, 22 residues, 1 model selected > select up 2707 atoms, 2779 bonds, 330 residues, 1 model selected > save > /home/venkatareddy/workspace/analysis_mcqeen_14062021/Rv2067c/paper_Rv2067c/manuscript/images_Rv2067c_manuscript/6nj9_dot1L.pdb > selectedOnly true relModel #1 > open > /home/venkatareddy/workspace/analysis_mcqeen_14062021/Rv2067c/paper_Rv2067c/manuscript/images_Rv2067c_manuscript/6nj9_dot1L.pdb Summary of feedback from opening /home/venkatareddy/workspace/analysis_mcqeen_14062021/Rv2067c/paper_Rv2067c/manuscript/images_Rv2067c_manuscript/6nj9_dot1L.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 44 LYS A 56 1 13 Start residue of secondary structure not found: HELIX 2 2 ARG A 63 ALA A 75 1 13 Start residue of secondary structure not found: HELIX 3 3 GLN A 76 PHE A 78 1 3 Start residue of secondary structure not found: HELIX 4 4 GLN A 85 ALA A 114 1 30 Start residue of secondary structure not found: HELIX 5 5 NLE A 120 ARG A 131 1 12 82 messages similar to the above omitted Chain information for 6nj9_dot1L.pdb #2 --- Chain | Description K | No description available > hide #!1 models > select #2 2707 atoms, 2779 bonds, 330 residues, 1 model selected > rainbow sel > select clear > select #2/K:500@CE 1 atom, 1 residue, 1 model selected > select up 27 atoms, 29 bonds, 1 residue, 1 model selected > style sel ball Changed 27 atom styles > select clear > show #2 surfaces > hide #!2 surfaces > select #2 2707 atoms, 2779 bonds, 330 residues, 1 model selected > color (#!2 & sel) orange > select clear > show #!2 surfaces > lighting soft > select #2/K:500@N6 1 atom, 1 residue, 1 model selected > select up 27 atoms, 29 bonds, 1 residue, 1 model selected > style sel sphere Changed 27 atom styles > color sel byhetero > color sel byatom > select clear > lighting simple > lighting full > lighting soft > lighting simple [Repeated 1 time(s)] > lighting soft > lighting simple > hide #!2 surfaces > select clear > select #2/K:130 7 atoms, 7 bonds, 1 residue, 1 model selected > select up 100 atoms, 104 bonds, 12 residues, 2 models selected > ui tool show ""Color Actions"" > color sel light coral > select #2 2707 atoms, 2779 bonds, 330 residues, 1 model selected > ~select #2 1 model selected > select #2 2707 atoms, 2779 bonds, 330 residues, 1 model selected > color sel yellow > color sel khaki > select clear > select #2/K:130 7 atoms, 7 bonds, 1 residue, 1 model selected > select up 100 atoms, 104 bonds, 12 residues, 2 models selected > color sel light coral > select clear > select #2/K:243 11 atoms, 11 bonds, 1 residue, 1 model selected > select up 32 atoms, 32 bonds, 4 residues, 2 models selected > color sel teal > select clear [Repeated 1 time(s)] > select #2/K:308 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 148 atoms, 153 bonds, 19 residues, 2 models selected > color sel fire brick > select clear > show #!2 surfaces > transparency 20 > transparency 30 > hide #!2 surfaces > show #!2 surfaces > transparency 0 > surface #2 gridSpacing 0.3 > select #2/K:500@CE 1 atom, 1 residue, 1 model selected > select up 27 atoms, 29 bonds, 1 residue, 1 model selected > select up 2707 atoms, 2779 bonds, 330 residues, 1 model selected > select down 27 atoms, 29 bonds, 1 residue, 2 models selected > color sel byatom > select clear > hide #!2 surfaces > select #2/K:245 11 atoms, 11 bonds, 1 residue, 1 model selected > color sel teal > show sel surfaces > select clear > show #!2 surfaces > hide #!2 surfaces > select #2/K:245 11 atoms, 11 bonds, 1 residue, 1 model selected > color sel khaki > select clear > show #!2 surfaces > lighting soft [Repeated 1 time(s)] > lighting full > lighting simple > lighting soft > lighting gentle > lighting soft > select #2/K:500@CE 1 atom, 1 residue, 1 model selected > select clear > select #2/K:500@CE 1 atom, 1 residue, 1 model selected > select clear > lighting simple > lighting soft > lighting simple > lighting full > lighting simple > lighting full > lighting soft > select #2/K:500@CE 1 atom, 1 residue, 1 model selected > clip front 0 position #2:sam@ce > clip front -1 position #2:sam@ce > clip front 1 position #2:sam@ce > clip model #2:sam false > select clear > ~clip > transparency 20 > lighting soft > hide #!2 surfaces > clip front 1 position #2:sam@ce > show #!2 surfaces > transparency 0 > clip front 0 position #2:sam@ce > clip front -1 position #2:sam@ce > clip front -2 position #2:sam@ce > ~clip > hide #!2 surfaces > select clear > select #2/K:129 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 100 atoms, 104 bonds, 12 residues, 2 models selected > color sel blue > select clear [Repeated 1 time(s)] > select #2/K:243 11 atoms, 11 bonds, 1 residue, 1 model selected > select up 32 atoms, 32 bonds, 4 residues, 2 models selected > color sel tomato > color sel cornflower blue > select add #2/K:136 44 atoms, 44 bonds, 5 residues, 2 models selected > select up 132 atoms, 136 bonds, 16 residues, 2 models selected > select add #2/K:295 141 atoms, 144 bonds, 17 residues, 2 models selected > select up 280 atoms, 289 bonds, 35 residues, 2 models selected > show sel surfaces > select clear > show #!2 surfaces > select #2/K:243@CE2 1 atom, 1 residue, 1 model selected > select up 11 atoms, 11 bonds, 1 residue, 2 models selected > select up 32 atoms, 32 bonds, 4 residues, 2 models selected > color sel chartreuse > color sel green > color sel spring green > select #2/K:306@OG1 1 atom, 1 residue, 1 model selected > select up 7 atoms, 6 bonds, 1 residue, 2 models selected > select up 148 atoms, 153 bonds, 19 residues, 2 models selected > color sel deep pink > color sel dark violet > color sel hot pink > color sel burly wood > color sel pale goldenrod > color sel violet > color sel light green > color sel dark sea green > color sel gray > color sel orchid > color sel blue violet > color sel deep pink > color sel magenta > color sel tomato > lighting simple > select clear > select add #2/K:136@N 1 atom, 1 residue, 1 model selected > select up 12 atoms, 12 bonds, 1 residue, 2 models selected > select up 100 atoms, 104 bonds, 12 residues, 2 models selected > select add #2/K:243@CE2 101 atoms, 104 bonds, 13 residues, 2 models selected > select up 111 atoms, 115 bonds, 13 residues, 2 models selected > select up 132 atoms, 136 bonds, 16 residues, 2 models selected > lighting soft > set bgColor white > select clear > select #2.1 2680 atoms, 329 residues, 1 model selected > ~select #2.1 1 model selected > select #2 2707 atoms, 2779 bonds, 330 residues, 1 model selected > ui tool show ""Color Actions"" > color sel wheat > color sel yellow > color sel gold > color sel orange > color sel sandy brown > color sel goldenrod > color sel orange > color sel gold > color sel green yellow > color sel goldenrod [Repeated 1 time(s)] > color sel sandy brown > color sel indian red > color sel coral > color sel dark salmon > color sel salmon > color sel dark salmon > color sel light salmon > color sel wheat > graphics silhouettes true > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting flat > lighting full > lighting soft > lighting simple > lighting soft [Repeated 1 time(s)] > color sel goldenrod [Repeated 2 time(s)] > color sel sandy brown > color sel goldenrod > select clear > hide #!2 surfaces > graphics silhouettes false > select clear > select #2/K:137 4 atoms, 3 bonds, 1 residue, 1 model selected > select up 100 atoms, 104 bonds, 12 residues, 2 models selected > color sel green > color sel chartreuse > color sel spring green > color sel lime green > color sel lime > color sel medium sea green > select #2/K:243 11 atoms, 11 bonds, 1 residue, 1 model selected > select up 32 atoms, 32 bonds, 4 residues, 2 models selected > color sel fire brick > select #2/K:306 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 148 atoms, 153 bonds, 19 residues, 2 models selected > color sel slate blue > select clear > show #!2 surfaces > lighting simple > lighting soft > lighting simple > select #2/K:307@N 1 atom, 1 residue, 1 model selected > select up 4 atoms, 3 bonds, 1 residue, 2 models selected > select up 148 atoms, 153 bonds, 19 residues, 2 models selected > select add #2/K:243@CE2 149 atoms, 153 bonds, 20 residues, 2 models selected > select up 159 atoms, 164 bonds, 20 residues, 2 models selected > select up 180 atoms, 185 bonds, 23 residues, 2 models selected > select add #2/K:131@CZ 181 atoms, 185 bonds, 24 residues, 2 models selected > select up 191 atoms, 196 bonds, 24 residues, 2 models selected > select up 280 atoms, 289 bonds, 35 residues, 2 models selected > transparency sel 20 > transparency sel 30 > transparency sel 50 > select clear > transparency 50 > select clear [Repeated 2 time(s)] > hide #!2 surfaces > select clear > select #2/K:500@CE 1 atom, 1 residue, 1 model selected > select up 27 atoms, 29 bonds, 1 residue, 1 model selected > color sel byatom > select clear > lighting soft > show #!2 surfaces > transparency 0 > select clear [Repeated 1 time(s)] > hide #!2 surfaces > select #2/K:135 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 100 atoms, 104 bonds, 12 residues, 2 models selected > select add #2/K:312 112 atoms, 116 bonds, 13 residues, 2 models selected > select up 248 atoms, 257 bonds, 31 residues, 2 models selected > select add #2/K:243 259 atoms, 268 bonds, 32 residues, 2 models selected > select up 280 atoms, 289 bonds, 35 residues, 2 models selected > show sel surfaces > select clear [Repeated 1 time(s)] > surface #2 probeRadius 1.2 gridSpacing 0.3 > select clear [Repeated 1 time(s)] > hide #!2 surfaces > select #2/K:273 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 138 atoms, 141 bonds, 17 residues, 2 models selected > show sel surfaces > color sel light coral > select clear > show #!2 surfaces > select #2/K:274@CG 1 atom, 1 residue, 1 model selected > select up 7 atoms, 7 bonds, 1 residue, 2 models selected > select up 138 atoms, 141 bonds, 17 residues, 2 models selected > color sel violet > color sel deep pink > color sel magenta > color sel blue violet > color sel hot pink > color sel dark salmon > color sel medium turquoise > select clear > show #!1 models > select #1 18814 atoms, 19780 bonds, 371 pseudobonds, 1884 residues, 2 models selected > surface #1 probRadius 1.2 gridSpacing 0.3 Expected a keyword > surface #1 probeRadius 1.2 gridSpacing 0.3 > select clear > hide #!2 models > select #1/K:150@OE2 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 2 models selected > select up 95 atoms, 95 bonds, 12 residues, 2 models selected > select up 2707 atoms, 2779 bonds, 330 residues, 2 models selected > hide sel surfaces > select clear [Repeated 1 time(s)] > select #1/K:273 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 138 atoms, 141 bonds, 17 residues, 2 models selected > color sel maroon > color sel crimson > color sel red > show sel surfaces > select clear > select #1/K:294 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/K:293 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 33 atoms, 32 bonds, 4 residues, 2 models selected > select up 2707 atoms, 2779 bonds, 330 residues, 2 models selected > show sel surfaces > select clear > hide #!1 cartoons [Repeated 1 time(s)] > show #!1 cartoons > hide #!1 surfaces > color #1 bychain > select clear [Repeated 1 time(s)] > select #1/M:181 10 atoms, 10 bonds, 1 residue, 1 model selected > select up 43 atoms, 45 bonds, 5 residues, 2 models selected > select up 2707 atoms, 2779 bonds, 330 residues, 2 models selected > select add #1/N:32 2715 atoms, 2786 bonds, 331 residues, 2 models selected > select up 2816 atoms, 2887 bonds, 344 residues, 3 models selected > select up 3304 atoms, 3382 bonds, 405 residues, 3 models selected > delete sel > save > /home/venkatareddy/workspace/analysis_mcqeen_14062021/Rv2067c/paper_Rv2067c/manuscript/images_Rv2067c_manuscript/6nj9.pdb > models #1 > hide #!1 atoms > select #1:sam 27 atoms, 29 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 27 atom styles > color sel byatom > select clear > select #1/E:79 8 atoms, 7 bonds, 1 residue, 1 model selected > style sel stick Changed 8 atom styles > show sel atoms > ui tool show Rotamers > swapaa interactive sel LYS rotLib Dunbrack 6nj9 #1/E NLE 79: phi -56.8, psi -32.8 trans Changed 438 bond radii > swapaa #1/E:79 LYS criteria 2 rotLib Dunbrack Using Dunbrack library 6nj9 #1/E NLE 79: phi -56.8, psi -32.8 trans Applying LYS rotamer (chi angles: -175.3 176.1 179.1 180.0) to 6nj9 #1/E LYS 79 > style sel sphere Changed 4 atom styles > style sel sphere Changed 4 atom styles > style sel stick Changed 4 atom styles > select #1/E:79@NZ 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel byhetero > select clear [Repeated 1 time(s)] > lighting simple > lighting full > lighting simple > select #1/K:79 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 198 atoms, 202 bonds, 23 residues, 2 models selected > select up 2707 atoms, 2779 bonds, 330 residues, 2 models selected > color (#!1 & sel) orange > select clear > set bgColor black > set bgColor white > lighting soft > lighting flat > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting flat > lighting shadows true intensity 0.5 > lighting soft > graphics silhouettes false > graphics silhouettes true > surface #1 > lighting soft > lighting simple > lighting full > lighting shadows false > hide #!1 surfaces > graphics silhouettes false > lighting soft > lighting flat > lighting shadows true intensity 0.5 > graphics silhouettes false > lighting soft > graphics silhouettes true > select #1/K:500@N6 1 atom, 1 residue, 1 model selected > select up 27 atoms, 29 bonds, 1 residue, 1 model selected > color sel byatom > select clear > select #1/K:282 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 11 atom styles > color sel byhetero > style sel ball Changed 11 atom styles > select clear > lighting simple > select #1/G:56 9 atoms, 8 bonds, 1 residue, 1 model selected > select clear > lighting soft > view #1 > select #1/E:79@NZ 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 2 models selected > style sel ball Changed 9 atom styles > select clear > lighting soft > lighting full > graphics silhouettes false > lighting simple > open 7k6q 7k6q title: Active state Dot1 bound to the H4K16ac nucleosome [more info...] Chain information for 7k6q #3 --- Chain | Description | UniProt A E | Histone H3.2 | H32_XENLA B F | Histone H4 | H4_XENLA C G | Histone H2A type 1 | H2A1_XENLA D H | Histone H2B 1.1 | H2B11_XENLA I | DNA (146-mer) | J | DNA (146-mer) | K | Histone-lysine N-methyltransferase, H3 lysine-79 specific | DOT1_YEAST L | Ubiquitin | UBC_HUMAN Non-standard residues in 7k6q #3 --- SAM — S-adenosylmethionine > mmaker #3 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 6nj9, chain C (#1) with 7k6q, chain G (#3), sequence alignment score = 511.2 RMSD between 107 pruned atom pairs is 0.603 angstroms; (across all 107 pairs: 0.603) > show #!1,3 cartoons > hide #!1,3 atoms > select clear > hide #!3 models > show #!3 models > select #3/K:260 5 atoms, 4 bonds, 1 residue, 1 model selected > select #3/k:252-264 94 atoms, 96 bonds, 13 residues, 1 model selected > color sel red > select clear [Repeated 1 time(s)] > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > select #1/L:70 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 48 atoms, 48 bonds, 6 residues, 2 models selected > select up 597 atoms, 603 bonds, 75 residues, 2 models selected > mlp sel Map values for surface ""6nj9_L SES surface"": minimum -28.06, mean -3.871, maximum 24.51 To also show corresponding color key, enter the above mlp command and add key true > select clear > lighting soft [Repeated 1 time(s)] > lighting full > lighting simple > select #1/K:324 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 103 atoms, 104 bonds, 12 residues, 2 models selected > mlp sel Map values for surface ""6nj9_K SES surface"": minimum -29.35, mean -3.751, maximum 26.98 To also show corresponding color key, enter the above mlp command and add key true > select add #1/K:332 110 atoms, 111 bonds, 13 residues, 2 models selected > select up 118 atoms, 120 bonds, 14 residues, 2 models selected > mlp sel Map values for surface ""6nj9_K SES surface"": minimum -29.35, mean -3.751, maximum 26.98 To also show corresponding color key, enter the above mlp command and add key true > hide sel surfaces > select clear > select #1/L:9@O 1 atom, 1 residue, 1 model selected > select up 7 atoms, 6 bonds, 1 residue, 2 models selected > select up 35 atoms, 34 bonds, 5 residues, 2 models selected > select up 597 atoms, 603 bonds, 75 residues, 2 models selected > hide sel surfaces > select clear > select #1/L:71 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 8 atom styles > lighting soft > select clear > graphics silhouettes true > show #!2 models > hide #!1 models > select #2/K:500@CE 1 atom, 1 residue, 1 model selected > cofr sel > select clear > hide #!2 models > show #!2 models > hide #2.1 models Drag select of 46 atoms, 187 residues, 24 bonds > select clear Drag select of 2 residues > select clear Drag select of 17 atoms, 162 residues, 8 bonds > show sel surfaces > select clear Drag select of 6nj9_dot1L.pdb_K SES surface, 363400 of 891434 triangles, 21 atoms, 161 residues, 15 bonds > hide sel surfaces > select clear Drag select of 6nj9_dot1L.pdb_K SES surface, 264264 of 891434 triangles, 70 atoms, 278 residues, 37 bonds > hide sel surfaces > select clear [Repeated 1 time(s)] > select #2.1 2680 atoms, 329 residues, 1 model selected > show sel surfaces > select clear > clip back 0 position #2:sam@sd > transparency #2 50 > lighting simple > lighting soft > lighting simple > graphics silhouettes false > transparency #2 20 > graphics driver OpenGL version: 3.3.0 NVIDIA 460.91.03 OpenGL renderer: GeForce GTX 1050 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation > graphics quality Quality 1, atom triangles 2000, bond triangles 160, ribbon divisions 20 > graphics rate Maximum framerate 60 > graphics quality 2 > graphics quality 1 > lighting soft > graphics quality 2 > select #2/K:212 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > style sel ball Changed 2 atom styles > select clear > graphics silhouettes true > graphics silhouettes false > graphics quality 1 > graphics quality 3 > select #2/K:212@NZ 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 2 models selected > hide sel atoms > select clear > lighting simple > catroon style #2 Unknown command: catroon style #2 > graphics quality catroon style #2 Expected a number or a keyword > cartoon > cartoon style 6nj9 #1 \- helix mode=default xsection=round width=2 height=0.4 arrow=False arrow scale=2 \- strand mode=default xsection=square width=2 height=0.4 arrow=True arrow scale=2 \- coil xsection=round width=0.4 height=0.4 \- nucleic xsection=square width=0.4 height=2 \- divisions=20 \- oval parameters: sides=12 \- barbell parameters: sides=18 scale=0.5 6nj9_dot1L.pdb #2 \- helix mode=default xsection=round width=2 height=0.4 arrow=False arrow scale=2 \- strand mode=default xsection=square width=2 height=0.4 arrow=True arrow scale=2 \- coil xsection=round width=0.4 height=0.4 \- nucleic xsection=square width=0.4 height=2 \- divisions=20 \- oval parameters: sides=12 \- barbell parameters: sides=18 scale=0.5 7k6q #3 \- helix mode=default xsection=round width=2 height=0.4 arrow=False arrow scale=2 \- strand mode=default xsection=square width=2 height=0.4 arrow=True arrow scale=2 \- coil xsection=round width=0.4 height=0.4 \- nucleic xsection=square width=0.4 height=2 \- divisions=20 \- oval parameters: sides=12 \- barbell parameters: sides=18 scale=0.5 > cartoon style #2 width 1 > cartoon style #2 width 2 > cartoon style #2 width 3 > cartoon style #2 width 1.5 > cartoon style #2 width 2 > cartoon style #2 width 1.5 > cartoon style #2 width 1.8 > cartoon style #2 width 2 > cartoon style #2 width 2 thickness 1 > cartoon style #2 width 2 thickness 2 > cartoon style #2 width 2 thickness 0.5 > cartoon style #2 width 2 thickness 0.4 > lighting soft > graphics silhouettes true > lighting shadows true intensity 0.5 > lighting simple > lighting shadows true > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting full > lighting simple > view orient > lighting Intensity: 1 Direction: 0.577,-0.577,-0.577 Color: 100,100,100 Fill intensity: 0.5 Fill direction: -0.2,-0.2,-0.959 Fill color: 100,100,100 Ambient intensity: 0.4 Ambient color: 100,100,100 Depth cue: 1, start 0.5, end 1, color 100,100,100 Shadow: False (depth map size 2048, depth bias 0.005) Multishadows: 0 (max 1024, depth map size 1024, depth bias 0.01) > lighting soft > transparency 0 > ~clip > lighting Intensity: 0 Direction: 0.577,-0.577,-0.577 Color: 100,100,100 Fill intensity: 0 Fill direction: -0.2,-0.2,-0.959 Fill color: 100,100,100 Ambient intensity: 1.5 Ambient color: 100,100,100 Depth cue: 1, start 0.5, end 1, color 100,100,100 Shadow: False (depth map size 2048, depth bias 0.005) Multishadows: 64 (max 1024, depth map size 1024, depth bias 0.01) > lighting soft intensity 1 > lighting soft intensity 0 > lighting soft intensity 0 fillIntensity 1 > lighting soft intensity 0 fillIntensity 0 > lighting soft intensity 0 fillIntensity 0.2 > lighting soft intensity 0 fillIntensity 0.3 > lighting soft intensity 0 fillIntensity 0.4 > lighting soft intensity 0 fillIntensity 0 > lighting soft intensity 0 fillIntensity 0 Shadow true Expected a keyword > lighting soft intensity 0 fillIntensity 0 shadows true > lighting soft intensity 0 fillIntensity 0 shadows false > lighting soft > lighting gentle > lighting Intensity: 0 Direction: 0.577,-0.577,-0.577 Color: 100,100,100 Fill intensity: 0 Fill direction: -0.2,-0.2,-0.959 Fill color: 100,100,100 Ambient intensity: 1.5 Ambient color: 100,100,100 Depth cue: 1, start 0.5, end 1, color 100,100,100 Shadow: False (depth map size 2048, depth bias 0.005) Multishadows: 64 (max 1024, depth map size 128, depth bias 0.05) > graphics silhouettes false > set subdivision 3 > select #2/K:500@CE 1 atom, 1 residue, 1 model selected > color sel white > select clear > select #2/K:500@CE 1 atom, 1 residue, 1 model selected > select clear > select #2/K:500@CE 1 atom, 1 residue, 1 model selected > select up 27 atoms, 29 bonds, 1 residue, 1 model selected > select up 2707 atoms, 2779 bonds, 330 residues, 1 model selected > select clear > select #2/K:500@N7 1 atom, 1 residue, 1 model selected > select up 27 atoms, 29 bonds, 1 residue, 1 model selected > save > /home/venkatareddy/workspace/analysis_mcqeen_14062021/Rv2067c/paper_Rv2067c/manuscript/images_Rv2067c_manuscript/sam.pdb > selectedOnly true relModel #2 > select clear > select #2/K:500@CE 1 atom, 1 residue, 1 model selected > select up 27 atoms, 29 bonds, 1 residue, 1 model selected > select up 2707 atoms, 2779 bonds, 330 residues, 1 model selected > select down 27 atoms, 29 bonds, 1 residue, 2 models selected > hide sel > select clear > open sam.pdb Summary of feedback from opening sam.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 44 LYS A 56 1 13 Start residue of secondary structure not found: HELIX 2 2 ARG A 63 ALA A 75 1 13 Start residue of secondary structure not found: HELIX 3 3 GLN A 76 PHE A 78 1 3 Start residue of secondary structure not found: HELIX 4 4 GLN A 85 ALA A 114 1 30 Start residue of secondary structure not found: HELIX 5 5 NLE A 120 ARG A 131 1 12 74 messages similar to the above omitted > select #4 27 atoms, 29 bonds, 1 residue, 1 model selected > style sel sphere Changed 27 atom styles > lighting model #4 simple Expected a keyword > select clear > select #4/K:500@CE 1 atom, 1 residue, 1 model selected > hide #!2 models > select clear > show #!2 models > select #4/K:500@CE 1 atom, 1 residue, 1 model selected > select up 27 atoms, 29 bonds, 1 residue, 1 model selected > color sel byatom > color sel white > select clear > select #4/K:500@CE 1 atom, 1 residue, 1 model selected > select up 27 atoms, 29 bonds, 1 residue, 1 model selected > style sel ball Changed 27 atom styles > select clear > select #4/K:500@CE 1 atom, 1 residue, 1 model selected > select up 27 atoms, 29 bonds, 1 residue, 1 model selected > color sel byhetero > select clear > select #4/K:500@CE 1 atom, 1 residue, 1 model selected > select up 27 atoms, 29 bonds, 1 residue, 1 model selected > color sel yellow > select clear > select #4/K:500@CE 1 atom, 1 residue, 1 model selected > select up 27 atoms, 29 bonds, 1 residue, 1 model selected > color sel light gray > color sel lime > select clear > select #4/K:500@CE 1 atom, 1 residue, 1 model selected > select up 27 atoms, 29 bonds, 1 residue, 1 model selected > color sel white > select clear > graphics silhouettes true > select clear > select #4/K:500@CE 1 atom, 1 residue, 1 model selected > select up 27 atoms, 29 bonds, 1 residue, 1 model selected > style sel sphere Changed 27 atom styles > select clear > select #4/K:500@CE 1 atom, 1 residue, 1 model selected > select up 27 atoms, 29 bonds, 1 residue, 1 model selected > color sel byhetero > select clear > close #2 > close #4 > show #!1 models > close #3 > view > show surfaces > color bychain > select clear [Repeated 1 time(s)] > hide surfaces > lighting simple > select /K:118 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 138 atoms, 140 bonds, 17 residues, 2 models selected > select up 2707 atoms, 2779 bonds, 330 residues, 2 models selected > ui tool show ""Color Actions"" > color sel goldenrod > color sel khaki > color sel pale goldenrod > color sel peach puff > color sel navajo white > color sel yellow > color sel gold > color sel orange > color sel dark orange > select clear > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > lighting shadows true > lighting shadows false > graphics silhouettes true > graphics silhouettes false > lighting soft > select /L:42 11 atoms, 10 bonds, 1 residue, 1 model selected > select up 47 atoms, 47 bonds, 5 residues, 2 models selected > select up 597 atoms, 603 bonds, 75 residues, 2 models selected > color sel > color > select /E:72 11 atoms, 10 bonds, 1 residue, 1 model selected > select /a,e 1633 atoms, 1657 bonds, 198 residues, 1 model selected > color sel lime green > color sel spring green > color sel lawn green > color sel chartreuse [Repeated 1 time(s)] > color sel green > color sel lime > color sel green > color sel chartreuse > color sel lime green > color sel forest green > color sel green > color sel lawn green > color sel spring green > color sel lime green > select clear > select /b,f 1416 atoms, 1432 bonds, 176 residues, 1 model selected > color sel red > color sel orange red > color sel crimson > color sel tomato > color sel brown > color sel chocolate [Repeated 2 time(s)] > color sel indian red > color sel dodger blue > color sel turquoise > color sel rebecca purple > color sel medium slate blue > color sel pale goldenrod > color sel khaki > color sel violet > select /a,e 1633 atoms, 1657 bonds, 198 residues, 1 model selected > color sel violet > color sel pale goldenrod > color sel spring green > color sel sea green > color sel royal blue > color sel dark khaki > color sel peru > color sel wheat > color sel lime green > color sel spring green > color sel medium sea green > color sel magenta > color sel orchid > color sel crimson > select /b,f 1416 atoms, 1432 bonds, 176 residues, 1 model selected > color sel pale green > color sel medium spring green > color sel dark turquoise [Repeated 1 time(s)] > color sel medium spring green > color sel dark turquoise > color sel dodger blue > color sel dark turquoise > select /c,g 1686 atoms, 1706 bonds, 218 residues, 1 model selected > color sel burly wood > color sel tan > color sel silver > color sel thistle > color sel salmon > color sel light coral [Repeated 1 time(s)] > color sel wheat > color sel tan > color sel rosy brown > color sel dark gray > color sel seashell > color sel lavender blush > color sel papaya whip > color sel blanched almond > color sel misty rose > color sel bisque > color sel moccasin > color sel navajo white > color sel peach puff > color sel pink > color sel thistle > color sel sandy brown > color sel dark salmon [Repeated 1 time(s)] > color sel peru > color sel light salmon > color sel dark khaki > color sel dark salmon > color sel wheat > color sel burly wood > color sel rosy brown > color sel tan > color sel pale violet red > color sel teal > color sel lime > color sel chocolate > color sel medium sea green > color sel dark orange > color sel yellow > color sel gold > color sel sandy brown [Repeated 1 time(s)] > color sel deep sky blue > color sel sandy brown > select /d,h 1486 atoms, 1508 bonds, 190 residues, 1 model selected > color sel gray > color sel dim gray > color sel red > color sel dark red > color sel dark cyan > color sel beige > color sel black > color sel dark green > color sel orchid > color sel medium orchid > color sel medium violet red > color sel medium orchid > color sel orchid > color sel blue violet > color sel hot pink > color sel dark violet > color sel deep pink > color sel magenta > color sel deep pink > color sel light sea green > color sel fire brick > color sel maroon > color sel dark olive green > color sel green > color sel steel blue > color sel green > color sel olive > select clear > select /L:71 8 atoms, 7 bonds, 1 residue, 1 model selected > select /l 597 atoms, 603 bonds, 75 residues, 1 model selected > color sel fire brick > color sel red > color sel orange red > color sel crimson > color sel dark red > color sel crimson > color sel dark red > color sel maroon > color sel fire brick > color sel tomato > color sel brown > color sel chocolate > color sel sienna > color sel saddle brown > color sel indian red > color sel yellow > color sel gold > color sel aquamarine > color sel crimson > color sel dim gray > color sel dark turquoise > color sel teal > select /k 2707 atoms, 2779 bonds, 330 residues, 1 model selected > color sel sandy brown > color sel goldenrod > color sel dark orange > color sel goldenrod > color sel crimson > color sel dark red > color sel crimson > color sel orange red > color sel dark red > color sel crimson > color sel sandy brown > color sel goldenrod > color sel green yellow > color sel dark orange [Repeated 1 time(s)] > color sel goldenrod > color sel green yellow > color sel dark orange > color sel orange > color sel indian red > color sel sienna > color sel coral > color sel saddle brown > color sel chocolate [Repeated 1 time(s)] > color sel brown [Repeated 1 time(s)] > color sel tomato > color sel fire brick > color sel maroon > color sel dark red > color sel crimson > color sel orange red > color sel red > select clear > select /I:126 22 atoms, 24 bonds, 1 residue, 1 model selected > select up 2975 atoms, 3333 bonds, 146 residues, 2 models selected > select /i,j 5986 atoms, 6714 bonds, 371 pseudobonds, 292 residues, 2 models selected > color sel gray > color sel dim gray > color sel medium slate blue > color sel slate blue > color sel dim gray > color sel gainsboro > color sel dim gray > color sel silver > color sel dim gray > color sel navy > color sel slate gray > show sel surfaces > color sel slate gray > color sel dim gray > hide sel surfaces > select /k 2707 atoms, 2779 bonds, 330 residues, 1 model selected > color sel crimson [Repeated 1 time(s)] > color sel dark red > color sel crimson > select /a,e 1633 atoms, 1657 bonds, 198 residues, 1 model selected > color sel goldenrod > color sel green yellow [Repeated 1 time(s)] > color sel dark orange > color sel green yellow > color sel cyan > color sel blue > color sel cyan > color sel green yellow > color sel lime > color sel chartreuse > color sel lawn green > color sel green > color sel lime green > select /b,f 1416 atoms, 1432 bonds, 176 residues, 1 model selected > color sel dark orange > color sel forest green > color sel green > color sel saddle brown > color sel dark violet > color sel deep pink > color sel slate blue > color sel dark sea green > lighting simple > lighting soft > color sel dark cyan > color sel light slate gray > color sel slate blue [Repeated 1 time(s)] > color sel medium slate blue > color sel orange red > color sel tomato > color sel brown > color sel chocolate > color sel dark turquoise > color sel medium spring green > color sel dark turquoise > color sel medium slate blue > color sel dodger blue > color sel medium slate blue > color sel turquoise > color sel medium aquamarine > color sel teal > color sel medium slate blue > select /l 597 atoms, 603 bonds, 75 residues, 1 model selected > color sel khaki [Repeated 1 time(s)] > color sel wheat > color sel goldenrod > color sel sandy brown > color sel orange > color sel gold > color sel orange > color sel dark orange > color sel orange red > color sel gold > color sel orange [Repeated 1 time(s)] > color sel dark orange > color sel green yellow > color sel goldenrod > select clear > lighting full > lighting simple > select /l 597 atoms, 603 bonds, 75 residues, 1 model selected > lighting soft > color sel cyan > color sel teal > color sel medium aquamarine > color sel dark turquoise > color sel medium spring green > color sel dodger blue > color sel turquoise > color sel medium turquoise > color sel light sea green > color sel cornflower blue > color sel dark violet > color sel hot pink > color sel dark cyan > color sel cornflower blue > color sel dark cyan > color sel cornflower blue > lighting simple > lighting soft > set subdivision 3 > select :sam 27 atoms, 29 bonds, 1 residue, 1 model selected > show sel atoms > color sel byatom > select clear > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > graphics silhouettes true > lighting soft > graphics silhouettes false > graphics silhouettes true > save 6nj9_soft_1.png transparentBackground true > view name 1 > save 6nj9_interactions.cxs > view 1 > view > select /E:79 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms [Repeated 1 time(s)] > style sel ball Changed 9 atom styles > color sel byhetero > select clear > open 6nog.pdb 6nog.pdb title: Poised-state DOT1L bound to the H2B-ubiquitinated nucleosome [more info...] Chain information for 6nog.pdb #2 --- Chain | Description | UniProt A E | histone H3.2 | H32_XENLA B | histone H4 | H4_XENLA C | histone H2A type 1 | H2A1_XENLA D | H2B1.1 | H2B11_XENLA F | histone H4 | H4_XENLA G | histone H2A type 1 | H2A1_XENLA H | H2B1.1 | H2B11_XENLA I | 601 DNA strand 1 | J | 601 DNA strand 2 | K | histone-lysine N-methyltransferase, H3 lysine-79 specific | DOT1L_HUMAN L | ubiquitin | J3QS39_HUMAN > select #2 14929 atoms, 15798 bonds, 3 pseudobonds, 1416 residues, 2 models selected > show sel cartoons [Repeated 1 time(s)] > hide sel atoms > mmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 6nj9, chain K (#1) with 6nog.pdb, chain K (#2), sequence alignment score = 1455 RMSD between 282 pruned atom pairs is 0.889 angstroms; (across all 302 pairs: 1.183) > hide #!1 models > select clear > select #2/K:77 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 211 atoms, 215 bonds, 25 residues, 1 model selected > select up 2431 atoms, 2486 bonds, 302 residues, 1 model selected > delete sel > select #2/L:48 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 18 atoms, 17 bonds, 2 residues, 1 model selected > select up 593 atoms, 599 bonds, 74 residues, 1 model selected > delete sel > mmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 6nj9, chain C (#1) with 6nog.pdb, chain G (#2), sequence alignment score = 488.1 RMSD between 105 pruned atom pairs is 0.495 angstroms; (across all 105 pairs: 0.495) > show #!1 models > view 1 > select #1/K:500@CE 1 atom, 1 residue, 1 model selected > cofr sel > view 1 > select clear [Repeated 1 time(s)] > select #1/K:131 11 atoms, 11 bonds, 1 residue, 1 model selected > select add #1/K:305 25 atoms, 26 bonds, 2 residues, 2 models selected > show sel atoms > style sel stick Changed 25 atom styles > style sel ball Changed 25 atom styles > color sel byhetero > style sel sphere Changed 25 atom styles > select add #1/E:79@NZ 26 atoms, 26 bonds, 3 residues, 2 models selected > select up 34 atoms, 34 bonds, 3 residues, 3 models selected > style sel sphere Changed 34 atom styles > select add #1/K:500@SD 35 atoms, 34 bonds, 4 residues, 3 models selected > select up 61 atoms, 63 bonds, 4 residues, 3 models selected > style sel sphere Changed 61 atom styles > select add #2/A:79 70 atoms, 71 bonds, 5 residues, 4 models selected > show sel atoms > style sel ball Changed 70 atom styles > select clear [Repeated 1 time(s)] > select #2/A:79@CE 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 1 model selected > ui tool show Rotamers > swapaa interactive sel LYS rotLib Dunbrack 6nog.pdb #2/A LYS 79: phi -164.6, psi 127.3 trans Changed 438 bond radii > swapaa #2/A:79 LYS criteria 1 rotLib Dunbrack retain false Using Dunbrack library 6nog.pdb #2/A LYS 79: phi -164.6, psi 127.3 trans Applying LYS rotamer (chi angles: -175.7 175.9 179.5 -180.0) to 6nog.pdb #2/A LYS 79 > select #2/A:79@CE 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel byhetero > select clear > color #2/a,e lime green > color byhetero > color #2/b,f Medium Slate Blue Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > select #2/b,f 1272 atoms, 1286 bonds, 160 residues, 1 model selected > color sel medium slate blue > select #2/c,g 1609 atoms, 1629 bonds, 209 residues, 1 model selected > color sel sandy brown > select #2/d,h 1456 atoms, 1478 bonds, 187 residues, 1 model selected > color sel olive drab > color sel olive > select clear > select #2/i,j 5986 atoms, 6714 bonds, 292 residues, 1 model selected > color sel dim gray > select clear > hide #!2 models > show #!2 models > select #1/E:79@NZ 1 atom, 1 residue, 1 model selected > select add #1/K:500@CE 2 atoms, 2 residues, 2 models selected > distance sel Distance between 6nj9 #1/E LYS 79 NZ and /K SAM 500 CE: 2.332Å > close #3 > select clear > hide #!2 models > select add #1/K:131@CE2 1 atom, 1 residue, 1 model selected > select up 11 atoms, 11 bonds, 1 residue, 2 models selected > select add #1/K:305@CD1 12 atoms, 11 bonds, 2 residues, 2 models selected > select up 25 atoms, 26 bonds, 2 residues, 2 models selected > style sel sphere Changed 25 atom styles > select clear > select add #1/E:79@CG 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 2 models selected > style sel sphere Changed 9 atom styles > select clear > show #!2 models > select add #2/A:79@CG 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 1 model selected > style sel sphere Changed 9 atom styles > hide #!1 models > select clear > lighting simple > lighting full > lighting flat > lighting shadows true intensity 0.5 > lighting simple > lighting shadows true > lighting shadows false > lighting simple > show #!1 models > lighting soft > hide #!2 models > select #1/K:305@CB 1 atom, 1 residue, 1 model selected > select up 14 atoms, 15 bonds, 1 residue, 2 models selected > style sel ball Changed 14 atom styles > style sel sphere Changed 14 atom styles > select add #1/E:79@CA 15 atoms, 15 bonds, 2 residues, 2 models selected > select clear > select add #1/K:305@CB 1 atom, 1 residue, 1 model selected > select up 14 atoms, 15 bonds, 1 residue, 2 models selected > select add #1/K:131@CD2 15 atoms, 15 bonds, 2 residues, 2 models selected > select up 25 atoms, 26 bonds, 2 residues, 2 models selected > style sel ball Changed 25 atom styles > select clear > show #!2 models > hide #!2 models > hide #!1 models > show #!2 models > show #!1 models > hide #!2 models > select add #1/K:305@CG 1 atom, 1 residue, 1 model selected > select up 14 atoms, 15 bonds, 1 residue, 2 models selected > select add #1/K:131@CD2 15 atoms, 15 bonds, 2 residues, 2 models selected > select up 25 atoms, 26 bonds, 2 residues, 2 models selected > style sel sphere Changed 25 atom styles > select clear > lighting simple > lighting soft > lighting simple > graphics silhouettes false > graphics silhouettes true > lighting soft > lighting simple > lighting soft > lighting gentle > graphics silhouettes false > graphics silhouettes true > lighting gentle depthCue true > lighting gentle depthCue true depthCueStart 0.2 depthCueEnd 1.0 > lighting gentle depthCue true depthCueStart 0.5 depthCueEnd 1.0 > lighting gentle depthCue true depthCueStart 0.3 depthCueEnd 1.0 > lighting gentle depthCue true depthCueStart 0.5 depthCueEnd 1.0 > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > lighting simple > save 6nj9_active_simple_1.png transparentBackground ture Invalid ""transparentBackground"" argument: Expected true or false (or 1 or 0) > save 6nj9_active_simple_1.png transparentBackground true > lighting soft > lighting simple > lighting soft > save 6nj9_active_soft_1.png transparentBackground true > save view lys79 Cannot determine format for 'view' > view name lys79 > lighting simple > graphics silhouettes false > graphics silhouettes true > lighting soft > lighting gentle > lighting soft > lighting gentle > lighting soft > lighting gentle [Repeated 1 time(s)] > lighting soft > lighting gentle > lighting soft > lighting simple > view 1 > lighting simple > show #!2 models > hide #!1 models > select #2/J:43 21 atoms, 23 bonds, 1 residue, 1 model selected > hide sel cartoons > select #2/J:44 21 atoms, 23 bonds, 1 residue, 1 model selected > select up 3011 atoms, 3381 bonds, 146 residues, 1 model selected > show sel cartoons > select clear > select #2/J:43 21 atoms, 23 bonds, 1 residue, 1 model selected > select add #2/J:44 42 atoms, 46 bonds, 2 residues, 1 model selected > select up 3011 atoms, 3381 bonds, 146 residues, 1 model selected > transparency sel 50 > select clear > select #2/J:43 21 atoms, 23 bonds, 1 residue, 1 model selected > select add #2/J:44 42 atoms, 46 bonds, 2 residues, 1 model selected > hide sel cartoons > select clear > show #!1 models > view 1 > show cartoons > select clear > view 1 > view name 2 > hide #!2 models > select #1/E:79@CA 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 2 models selected > style sel ball Changed 9 atom styles > style sel stick Changed 9 atom styles > style sel ball Changed 9 atom styles > select #1/K:127 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 57 atoms, 57 bonds, 7 residues, 2 models selected > transparency sel target c Missing or invalid ""percent"" argument: Expected a number > transparency sel 50 target c > select #1/K:128 12 atoms, 12 bonds, 1 residue, 1 model selected > select up 100 atoms, 104 bonds, 12 residues, 2 models selected > select up 2707 atoms, 2779 bonds, 330 residues, 2 models selected > select down 100 atoms, 104 bonds, 12 residues, 2 models selected > transparency sel 50 target c > select #1/K:129 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 100 atoms, 104 bonds, 12 residues, 2 models selected > select up 2707 atoms, 2779 bonds, 330 residues, 2 models selected > transparency sel 50 target c > select clear > lighting simple > lighting soft > transparency sel 70 target c > select clear > select #1/K:128 12 atoms, 12 bonds, 1 residue, 1 model selected > select up 100 atoms, 104 bonds, 12 residues, 2 models selected > select up 2707 atoms, 2779 bonds, 330 residues, 2 models selected > transparency sel 70 target c > lighting simple > select clear > select #1/K:134 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 100 atoms, 104 bonds, 12 residues, 2 models selected > select up 2707 atoms, 2779 bonds, 330 residues, 2 models selected > transparency sel 0 target c > select clear > select #1/K:132 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 100 atoms, 104 bonds, 12 residues, 2 models selected > ui tool show ""Color Actions"" > color sel medium turquoise > color sel turquoise > color sel dodger blue > color sel crimson > select clear > select #1/E:79@CB 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 2 models selected > style sel sphere Changed 9 atom styles > lighting soft > select clear > lighting soft > lighting full > lighting simple [Repeated 1 time(s)] > select #1/E:79@CA 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 2 models selected > transparency sel 50 target a > select clear > select #1/E:79@CB 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 2 models selected > transparency sel 0 target a > select clear > select #1/K:305@CB 1 atom, 1 residue, 1 model selected > select up 14 atoms, 15 bonds, 1 residue, 2 models selected > style sel ball Changed 14 atom styles > select clear > view 2 > select #1/K:305@CD1 1 atom, 1 residue, 1 model selected > select up 14 atoms, 15 bonds, 1 residue, 2 models selected > style sel sphere Changed 14 atom styles > select clear [Repeated 1 time(s)] > lighting full > lighting soft > lighting full > lighting shadows false > lighting flat [Repeated 1 time(s)] > lighting full > lighting shadows false > lighting shadows true > lighting shadows false > lighting full > lighting shadows false > lighting simple > lighting full > lighting simple > lighting Intensity: 1 Direction: 0.577,-0.577,-0.577 Color: 100,100,100 Fill intensity: 0.5 Fill direction: -0.2,-0.2,-0.959 Fill color: 100,100,100 Ambient intensity: 0.4 Ambient color: 100,100,100 Depth cue: 1, start 0.5, end 1, color 100,100,100 Shadow: False (depth map size 2048, depth bias 0.005) Multishadows: 0 (max 1024, depth map size 1024, depth bias 0.01) > lighting fillIntensity 1 > lighting fillIntensity 0.5 > lighting fillIntensity 0. > lighting fillIntensity 0.5 > lighting fillIntensity 0.2 > lighting fillIntensity 0.8 > graphics silhouettes false > lighting shadows true > lighting shadows false > lighting fillIntensity 0.5 > lighting soft > select clear > lighting Intensity: 0 Direction: 0.577,-0.577,-0.577 Color: 100,100,100 Fill intensity: 0 Fill direction: -0.2,-0.2,-0.959 Fill color: 100,100,100 Ambient intensity: 1.5 Ambient color: 100,100,100 Depth cue: 1, start 0.5, end 1, color 100,100,100 Shadow: False (depth map size 2048, depth bias 0.005) Multishadows: 64 (max 1024, depth map size 1024, depth bias 0.01) > lighting fillIntensity 0.2 > lighting gentle > lighting Intensity: 0 Direction: 0.577,-0.577,-0.577 Color: 100,100,100 Fill intensity: 0 Fill direction: -0.2,-0.2,-0.959 Fill color: 100,100,100 Ambient intensity: 1.5 Ambient color: 100,100,100 Depth cue: 1, start 0.5, end 1, color 100,100,100 Shadow: False (depth map size 2048, depth bias 0.005) Multishadows: 64 (max 1024, depth map size 128, depth bias 0.05) > lighting gentle > lighting soft > view 2 > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > set subdivision 3 > set subdivision 10 > set subdivision 1 > set subdivision 10 > lighting simple > graphics silhouettes false > lighting simple > lighting soft > save 6nj9_view2_k79_soft1.png transparentBackground true > view 2 > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > view list Named views: 1, 2, lys79 > view lys79 > view 2 > show #!2 models > hide #!1 models > select #2/A:79@NZ 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 1 model selected > style sel ball Changed 9 atom styles > style sel stick Changed 9 atom styles > style sel sphere Changed 9 atom styles > show #!1 models > select clear > hide #!2 models > view name lys79 > save 6nj9_view2_k79_soft1.png transparentBackground true > show #!2 models > hide #!1 models > save 6nj9_view2_k79_soft2.png transparentBackground true > view 2 > show #!1 models > hide #!2 models > graphics silhouettes true > save 6nj9_view2.png transparentBackground true > view name lys79 [Repeated 1 time(s)] > view 2 > view lys79 > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > save 6nj9_view2_k79_soft1.png transparentBackground true > show #!2 models > hide #!1 models > save 6nj9_view2_k79_soft2.png transparentBackground true > select #2/I:113 21 atoms, 23 bonds, 1 residue, 1 model selected > select add #2/I:95 40 atoms, 43 bonds, 2 residues, 1 model selected > distance sel Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got 40 > select clear > ui tool show ""Scale Bar"" > scalebar > scalebar 10 > lighting gentle > lighting soft Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/label/scalebar_gui.py"", line 61, in _color_changed self._update_scalebar() File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/label/scalebar_gui.py"", line 65, in _update_scalebar self._show_scalebar() File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/label/scalebar_gui.py"", line 70, in _show_scalebar options = self._changed_options() File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/label/scalebar_gui.py"", line 90, in _changed_options length = self._length.value File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/ui/widgets/composite.py"", line 185, in _get_value return self.string_to_value(self._line_edit.text()) ValueError: invalid literal for int() with base 10: '10lig' ValueError: invalid literal for int() with base 10: '10lig' File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/ui/widgets/composite.py"", line 185, in _get_value return self.string_to_value(self._line_edit.text()) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/label/scalebar_gui.py"", line 61, in _color_changed self._update_scalebar() File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/label/scalebar_gui.py"", line 65, in _update_scalebar self._show_scalebar() File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/label/scalebar_gui.py"", line 70, in _show_scalebar options = self._changed_options() File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/label/scalebar_gui.py"", line 90, in _changed_options length = self._length.value File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/ui/widgets/composite.py"", line 185, in _get_value return self.string_to_value(self._line_edit.text()) ValueError: invalid literal for int() with base 10: '10lig' ValueError: invalid literal for int() with base 10: '10lig' File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/ui/widgets/composite.py"", line 185, in _get_value return self.string_to_value(self._line_edit.text()) See log for complete Python traceback. > scalebar off Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/label/scalebar_gui.py"", line 65, in _update_scalebar self._show_scalebar() File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/label/scalebar_gui.py"", line 70, in _show_scalebar options = self._changed_options() File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/label/scalebar_gui.py"", line 90, in _changed_options length = self._length.value File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/ui/widgets/composite.py"", line 185, in _get_value return self.string_to_value(self._line_edit.text()) ValueError: invalid literal for int() with base 10: '10lig' ValueError: invalid literal for int() with base 10: '10lig' File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/ui/widgets/composite.py"", line 185, in _get_value return self.string_to_value(self._line_edit.text()) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/label/scalebar_gui.py"", line 65, in _update_scalebar self._show_scalebar() File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/label/scalebar_gui.py"", line 70, in _show_scalebar options = self._changed_options() File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/label/scalebar_gui.py"", line 90, in _changed_options length = self._length.value File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/ui/widgets/composite.py"", line 185, in _get_value return self.string_to_value(self._line_edit.text()) ValueError: invalid literal for int() with base 10: '10lig' ValueError: invalid literal for int() with base 10: '10lig' File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/ui/widgets/composite.py"", line 185, in _get_value return self.string_to_value(self._line_edit.text()) See log for complete Python traceback. > scalebar > scalebar 10 > save test_N10.png transparentBackground true supersample 10 > save test_N3.png transparentBackground true supersample 10 > save test_N3.png transparentBackground true > save test_ps01.png transparentBackground true pixelSize 0.1 > save test_ps001.png transparentBackground true pixelSize 0.01 > graphics silhouettes false > graphics silhouettes true > save test_ps005.png transparentBackground true pixelSize 0.05 > save test_ps002.png transparentBackground true pixelSize 0.02 > show #!1 models > hide #!4 models > view 2 > show #!4 models > hide #!2 models > hide #!4 models > select #1/K:131@CD2 1 atom, 1 residue, 1 model selected > view 2 > select clear > view 2 [Repeated 1 time(s)] > lighting soft > save 6nj9_view2ps002.png transparentBackground true > save 6nj9_view2ps002.png transparentBackground true pixelSize 0.02 > save 6nj9_interactions.cxs ——— End of log from Wed Dec 8 23:04:13 2021 ——— opened ChimeraX session > view 2 > save 6nj9_complex.png transparentBackground true pixelSize 0.1 > save 6nj9_complex.png transparentBackground true pixelSize 0.05 > hide #!1 atoms > save 6nj9_complex.png transparentBackground true pixelSize 0.05 > select :sam 27 atoms, 29 bonds, 1 residue, 1 model selected > show sel atoms > select clear > save 6nj9_complex.png transparentBackground true pixelSize 0.05 > view 2 > select add #1/K:131 11 atoms, 11 bonds, 1 residue, 1 model selected > select add #1/E:79 20 atoms, 19 bonds, 2 residues, 2 models selected > select add #1/K:305 34 atoms, 34 bonds, 3 residues, 3 models selected > show sel atoms > select clear [Repeated 1 time(s)] > select #1/F:19 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select clear [Repeated 1 time(s)] > view 2 > save 6nj9_k79_active.png transparentBackground true pixelSize 0.02 > hide #!1 atoms > select :sam 27 atoms, 29 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select #1/l:36,71,73 24 atoms, 21 bonds, 3 residues, 1 model selected > show sel atoms > style sel sphere Changed 24 atom styles > open > /home/venkatareddy/workspace/analysis_mcqeen_14062021/Rv2067c/paper_Rv2067c/manuscript/images_Rv2067c_manuscript/6nj9_dup.pdb > format pdb Chain information for 6nj9_dup.pdb #3 --- Chain | Description A | No description available B F | No description available C G | No description available D H | No description available E | No description available I | No description available J | No description available K | No description available L | No description available > select #3 15511 atoms, 16399 bonds, 1479 residues, 1 model selected > show sel cartoons > hide sel atoms > color #1/a,e lime green > color #1/b,f medium slate blue > color #3/c,g sandy brown > color #3/d,h olive > hide #!1 models > select clear > hide #3 models > show #!1 models > color #3/a,e lime green > color #3/b,f medium slate blue > show #3 models > hide #!1 models > color #3/k crimson > color #3/l cornflower blue > color #3/i,j dim gray > view 2 > show #!1 models > hide #!1 models > show #!1 models > select #3/l:36,71,73 24 atoms, 21 bonds, 3 residues, 1 model selected > show sel atoms > style sel stick Changed 24 atom styles > show #3/l:36,71,73 atoms > style #3/l:36,71,73 stick Changed 24 atom styles > show #1/l:36,71,73 atoms > style #3/l:36,71,73 sphere Changed 24 atom styles > style #3/l:36,71,73 sphere trans 50 traget a Expected a keyword > select #1/l:36,71,73 24 atoms, 21 bonds, 3 residues, 1 model selected > transparency sel 50 target a > hide #3 models > show #3 models > select #3/l:36,71,73 24 atoms, 21 bonds, 3 residues, 1 model selected > style sel stick Changed 24 atom styles > select clear > lighting simple > lighting soft > show #1/k:284,290,322,326 > transparency #1/k:284,290,322,326 50 target a > transparency #3/k:284,290,322,326 50 target a > style #1/k:284,290,322,326 stick Changed 35 atom styles > style #1/k:284,290,322,326 sphere Changed 35 atom styles > select #3/k:284,290,322,326 35 atoms, 32 bonds, 4 residues, 1 model selected > show sel atoms > style sel stick Changed 35 atom styles > transparency sel 0 target a > select clear > select #1/K:500@CE 1 atom, 1 residue, 1 model selected > cofr sel > select clear > view 2 > lighting simple [Repeated 1 time(s)] > view 2 > lighting soft > select #1/k:284,290,322,326 35 atoms, 32 bonds, 4 residues, 1 model selected > transparency sel 0 target a > select clear > select #1/L:73@CB 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 2 models selected > select add #1/L:71@CD1 9 atoms, 7 bonds, 2 residues, 2 models selected > select up 16 atoms, 14 bonds, 2 residues, 2 models selected > select add #1/L:36@CG2 17 atoms, 14 bonds, 3 residues, 2 models selected > select up 24 atoms, 21 bonds, 3 residues, 2 models selected > transparency sel 0 target a > select clear [Repeated 1 time(s)] > style #3#!1 stick Changed 31022 atom styles > style #3#!1 ball Changed 31022 atom styles > style #3#!1 sphere Changed 31022 atom styles > select #1/K:500@N1 1 atom, 1 residue, 1 model selected > select up 27 atoms, 29 bonds, 1 residue, 1 model selected > select up 2707 atoms, 2779 bonds, 330 residues, 1 model selected > select down 27 atoms, 29 bonds, 1 residue, 2 models selected > style sel stick Changed 27 atom styles > style sel ball Changed 27 atom styles > select clear > view 2 > save 6nj9_ub.png transparentBackground true pixelSize 0.02 > hide #3#!1 atoms > show #3#!1 atoms > hide #3#!1 atoms > select #1/k:284,290,322,326 35 atoms, 32 bonds, 4 residues, 1 model selected > style sel sphere Changed 35 atom styles > show sel atoms > select #1/l:36,71,73 24 atoms, 21 bonds, 3 residues, 1 model selected > show sel atoms > select clear > view name Ub > save 6nj9_interactions.cxs > hide #3#!1 atoms > show :sam atoms > select :sam 54 atoms, 58 bonds, 2 residues, 2 models selected > style sel ball Changed 54 atom styles > color sel byatom > select clear > view Ub > select clear > select #1/I:34 22 atoms, 24 bonds, 1 residue, 1 model selected > select up 2975 atoms, 3333 bonds, 146 residues, 2 models selected > select up 15511 atoms, 16399 bonds, 1479 residues, 2 models selected > select down 2975 atoms, 3333 bonds, 146 residues, 13 models selected > style sel sphere Changed 2975 atom styles > show sel atoms > select clear > scene dna save Unknown command: scene dna save > scene scene_name save Unknown command: scene scene_name save > scene Unknown command: scene > scene Unknown command: scene > scene list Unknown command: scene list > scene Unknown command: scene > hide #3#!1 atoms > select clear > select :sam 54 atoms, 58 bonds, 2 residues, 2 models selected > show sel atoms > select clear > select #1/K:500@CE 1 atom, 1 residue, 1 model selected > cofr sel > view 2 > select #1/K:282 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select #1/G:21 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 50 atoms, 49 bonds, 7 residues, 2 models selected > select up 843 atoms, 853 bonds, 109 residues, 2 models selected > select add #1/H:43 852 atoms, 861 bonds, 110 residues, 2 models selected > select up 958 atoms, 971 bonds, 122 residues, 3 models selected > select up 1586 atoms, 1607 bonds, 204 residues, 3 models selected > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 6nj9_G SES surface #1.8: minimum, -24.56, mean 2.46, maximum 19.16 Coulombic values for 6nj9_H SES surface #1.9: minimum, -14.09, mean 1.47, maximum 12.15 To also show corresponding color key, enter the above coulombic command and add key true > select clear > select #1/L:39 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 22 atoms, 23 bonds, 3 residues, 2 models selected > select up 597 atoms, 603 bonds, 75 residues, 2 models selected > hide sel cartoons > hide #3 models > hide #!1 models > show #3 models > hide #3 models > show #!1 models > select #1/G:22@CA 1 atom, 1 residue, 1 model selected > select up 4 atoms, 3 bonds, 1 residue, 2 models selected > select up 50 atoms, 49 bonds, 7 residues, 2 models selected > select up 843 atoms, 853 bonds, 109 residues, 2 models selected > select add #1/H:47@NE2 844 atoms, 853 bonds, 110 residues, 2 models selected > select up 852 atoms, 861 bonds, 110 residues, 3 models selected > select up 958 atoms, 971 bonds, 122 residues, 3 models selected > select up 1586 atoms, 1607 bonds, 204 residues, 3 models selected > transparency sel 50 > transparency sel 70 > transparency sel 30 > select clear > select #1/g:56 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > style sel sphere Changed 9 atom styles > style sel stick Changed 9 atom styles > style sel ball Changed 9 atom styles > style sel stick Changed 9 atom styles > select #1/h:113 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 9 atom styles > select clear > view 2 > transparency 0 > select #1/H:116@CD 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 2 models selected > select up 149 atoms, 151 bonds, 21 residues, 2 models selected > select up 743 atoms, 754 bonds, 95 residues, 2 models selected > select add #1/G:22@CA 744 atoms, 754 bonds, 96 residues, 2 models selected > select up 747 atoms, 757 bonds, 96 residues, 3 models selected > select up 793 atoms, 803 bonds, 102 residues, 3 models selected > select up 1586 atoms, 1607 bonds, 204 residues, 3 models selected > transparency sel 30 > transparency sel 50 > transparency sel 20 > view 2 > select clear > view name anchor > save 6nj9_interactions.cxs > view 2 [Repeated 1 time(s)] > view name anchor > cofr #1 > view 2 [Repeated 1 time(s)] > view name anchor > save 6nj9_anchor.png transparentBackground true pixelSize 0.02 > view 2 > hide surfaces > select #1/l 597 atoms, 603 bonds, 75 residues, 1 model selected > show sel cartoons > select clear > view 2 > view name h4 > select clear > select #1/K:197 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 198 atoms, 205 bonds, 22 residues, 2 models selected > select up 2707 atoms, 2779 bonds, 330 residues, 2 models selected > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 6nj9_K SES surface #1.12: minimum, -18.74, mean -2.63, maximum 9.74 To also show corresponding color key, enter the above coulombic command and add key true > select clear > select #1/f:17-19 32 atoms, 32 bonds, 3 residues, 1 model selected > show sel atoms > color sel byhetero > style sel stick Changed 32 atom styles > select clear > select #1/K:29@CE 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 2 models selected > select up 230 atoms, 240 bonds, 28 residues, 2 models selected > select up 2707 atoms, 2779 bonds, 330 residues, 2 models selected > transparency sel 50 > transparency sel 30 [Repeated 1 time(s)] > select #1/k:115,138 21 atoms, 20 bonds, 2 residues, 1 model selected > show sel atoms > style sel stick Changed 21 atom styles > color sel green target a > color sel cyan target a > color sel byhetero target a > select clear > view h4 > select clear > save 6nj9_h4tail.png transparentBackground true pixelSize 0.02 > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 11 atoms, 10 bonds, 1 residue, 2 models selected > style sel sphere Changed 11 atom styles > style sel stick Changed 11 atom styles > select clear > select #1/k:79 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms [Repeated 1 time(s)] > style sel stick Changed 8 atom styles > style sel sphere Changed 8 atom styles > select clear > select #1/E:79 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select clear > view h4 [Repeated 1 time(s)] > save 6nj9_h4tail.png transparentBackground true pixelSize 0.02 > view h4 > view name h4 > view h4 > view name h4 > view h4 > save 6nj9_h4tail.png transparentBackground true pixelSize 0.02 > view 2 > ~surface > select clear > hide #!1 atoms > select :sam 54 atoms, 58 bonds, 2 residues, 2 models selected > show sel atoms > select clear > show #!2 models > select #1/E:79 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select clear > show #3 models > hide #!1 models > select #3/K:124 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 57 atoms, 57 bonds, 7 residues, 1 model selected > select up 2707 atoms, 2779 bonds, 330 residues, 1 model selected > hide sel cartoons > select #3/K:500@C2' 1 atom, 1 residue, 1 model selected > select up 27 atoms, 29 bonds, 1 residue, 1 model selected > hide sel atoms > select #3/L:73 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 34 atoms, 33 bonds, 4 residues, 1 model selected > select up 597 atoms, 603 bonds, 75 residues, 1 model selected > hide sel cartoons > select #3/E:79 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select clear > view 2 > select clear > hide #3 models > show #3 models > hide #!2 models > select clear > show #!2 models > select #2/A:79@CE 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 54 atoms, 54 bonds, 6 residues, 1 model selected > select up 791 atoms, 803 bonds, 96 residues, 1 model selected > ui tool show ""Color Actions"" > color sel lime > color sel medium aquamarine > color sel teal > color sel steel blue > color sel medium turquoise > color sel gold > color sel orange > color sel green yellow > color sel goldenrod > color sel orange red > color sel red > color sel crimson > color sel maroon > color sel tomato > color sel fire brick > color sel brown > color sel chocolate > color sel byhetero > color sel lime green > color sel byhetero > color sel green > color sel dark cyan > color sel aquamarine > color sel lime green > select clear > select #2/A:79@NZ 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel byhetero > select clear > view 2 [Repeated 1 time(s)] > select #2/A:79@CE 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel hot pink > color sel deep pink > color sel magenta > color sel violet > color sel crimson > color sel orange red > color sel gold > color sel yellow > color sel byhetero > hide #!2 models > show #!2 models > hide #3 models > show #3 models > hide #3 models > show #!1 models > hide #!1 models > show #3 models > select up 54 atoms, 54 bonds, 6 residues, 1 model selected > select up 791 atoms, 803 bonds, 96 residues, 1 model selected > color sel gold > color sel byhetero > select clear > view 2 > save 6nj9_6nog_k79.png transparentBackground true pixelSize 0.02 > save 6nj9_6nog_k79_ps005.png transparentBackground true pixelSize 0.05 > show #!1 models > rename #3 6nj9_dup > open 6nj9_dup.pdb Chain information for 6nj9_dup.pdb #5 --- Chain | Description A | No description available B F | No description available C G | No description available D H | No description available E | No description available I | No description available J | No description available K | No description available L | No description available Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/core/triggerset.py"", line 134, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/ui/file_history.py"", line 93, in file_history_changed_cb self.update_html() File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/ui/file_history.py"", line 88, in update_html fhw.setHtml(html) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 272, in setHtml tf.write(bytes(html, ""utf-8"")) OSError: [Errno 28] No space left on device Error processing trigger ""file history changed"": OSError: [Errno 28] No space left on device File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 272, in setHtml tf.write(bytes(html, ""utf-8"")) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 460.91.03 OpenGL renderer: GeForce GTX 1050 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Model: OS: Ubuntu 20.04 focal Architecture: 64bit ELF Virutal Machine: none CPU: 8 Intel(R) Core(TM) i7-3770 CPU @ 3.40GHz Cache Size: 8192 KB Memory: total used free shared buff/cache available Mem: 15Gi 5.9Gi 4.2Gi 111Mi 5.5Gi 9.3Gi Swap: 15Gi 3.0Mi 15Gi Graphics: 01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP107 [GeForce GTX 1050 Ti] [10de:1c82] (rev a1) Subsystem: Gigabyte Technology Co., Ltd GP107 [GeForce GTX 1050 Ti] [1458:3764] Kernel driver in use: nvidia Locale: ('en_IN', 'ISO8859-1') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.10.8 cftime: 1.5.1.1 charset-normalizer: 2.0.7 ChimeraX-AddCharge: 1.2.1 ChimeraX-AddH: 2.1.10 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.30.2 ChimeraX-AtomicLibrary: 4.1.5 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3rc202111230539 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1 ChimeraX-LinuxSupport: 1.0 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.6.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13.7 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 distro: 1.6.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 line-profiler: 3.3.0 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: 21.3 ParmEd: 3.2.0 parso: 0.8.2 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.22 psutil: 5.8.0 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.2 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 }}} " defect closed normal Input/Output not a bug all ChimeraX