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Opened 6 years ago
Closed 6 years ago
#2035 closed defect (can't reproduce)
Nucleotides tethers: Bond drawing: cylinder and endpoint arrays differ in size
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Darwin-18.5.0-x86_64-i386-64bit ChimeraX Version: 0.9 (2019-06-01) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.9 (2019-06-01) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 6GEJ format mmCIF fromDatabase pdb 6gej title: Chromatin remodeller-nucleosome complex at 3.6 A resolution. [more info...] Chain information for 6gej #1 --- Chain | Description A B | Histone H3 C D | Histone H4 E F | Histone H2A.1 G H | Histone H2B.1 I | DNA (154-mer) J | DNA (154-mer) M | Helicase SWR1 R | Actin-like protein ARP6 S | Vacuolar protein sorting-associated protein 71 T V X | RuvB-like protein 1 U W Y | RuvB-like protein 2 Z | Vacuolar protein sorting-associated protein 72 Non-standard residues in 6gej #1 --- ADP — adenosine-5'-diphosphate BEF — beryllium trifluoride ion MG — magnesium ion ZN — zinc ion > set bgColor white > cartoon style modeHelix tube sides 24 > show selAtoms ribbons > hide selAtoms > toolshed show "Basic Actions" > hide /Z target c > hide /Y target c > hide /X target c > hide /W target c > hide /V target c > hide /U target c > hide /T target c > hide /S target c > hide /T target c > hide /M target c > hide /M target c > hide /S target c > hide /T target c > hide /U target c > hide /V target c > hide /Y target c > hide /Z target c > hide /R target c > nucleotides selAtoms tube/slab shape ellipsoid > show /I target abp > show /J target abp > lighting simple > lighting soft > lighting full > lighting shadows false > lighting shadows true > lighting full > lighting soft > lighting simple > lighting soft > lighting full > lighting soft > lighting flat > lighting flat > lighting full > lighting soft > lighting full > set silhouettes false > set silhouettes true > open 3psi 3psi title: Crystal Structure of the Spt6 core domain from Saccharomyces cerevisiae, Form Spt6(239-1451) [more info...] Chain information for 3psi #2 --- Chain | Description A | Transcription elongation factor SPT6 > view #2 clip false > select #2 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > hide #!2.1 models > toolshed show "Basic Actions" > show #2/A target s > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > select clear > lighting full > lighting shadows false > lighting shadows true > set silhouettes false > set silhouettes true > show #2/A target abp > hide #2/A target s > show #2/A target abp > show #2/A target s > style selAtoms sphere Changed 57379 atom styles > color selAtoms bychain > hide #2/A target s > show #2/A target s > color #2/A #6666ff target s > hide #2/A target abp > color #2/A #7f7f7f target s > color #2/A #666666 target s > color #2/A #ffff66 target s > color #2/A #fecc66 target s > color #2/A #fd6666 target s > ui mousemode rightMode label > label delete residues > ui mousemode rightMode label > label delete residues > toolshed show "Side View" > save session "/Users/aiste/Desktop/nucleosome and Spt6.cxs" > open 5OXV Summary of feedback from opening 5OXV fetched from pdb --- note | Fetching compressed mmCIF 5oxv from http://files.rcsb.org/download/5oxv.cif 5oxv title: Structure of the 4_601_157 tetranucleosome (C2 form) [more info...] Chain information for 5oxv #3 --- Chain | Description A E K O | Histone H3.2 B F L P | Histone H4 C G M Q | Histone H2A D H N R | Histone H2B 1.1 I | DNA STRAND 2 (601-based sequence model) J | DNA STRAND 1 (601-based sequence model) > select #3 24648 atoms, 26356 bonds, 731 pseudobonds, 1 model selected > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > cartoon style #5 > cartoon style #3 5oxv #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 > hide #3/A target abp > show #3/A target c > show #3/A target abp > hide #3/A target c Expected a keyword Unknown command: cmodeh tube sides 24 to #3 Expected a keyword Expected a keyword > cartoon style modeHelix tube sides 24 > hide #3/A target abp > show #3/A target c > show #3/B target c > show #3/C target c > show #3/D target c > show #3/E target c > show #3/F target c > show #3/G target c > show #3/H target c > show #3/K target c > show #3/L target c > show #3/N target c > show #3/Q target c > show #3/R target c > hide #3/R target abp > hide #3/Q target abp > hide #3/P target abp > hide #3/O target abp > hide #3/N target abp > hide #3/M target abp > hide #3/L target abp > hide #3/K target abp > hide #3/I target abp > hide #3/I target abp > show #3/I target abp > hide #3/H target abp > hide #3/G target abp > hide #3/L target abp > show #3/P target c > show #3/Q target c > show #3/R target c > show #3/R target c > show #3/Q target c > show #3/P target c > show #3/N target c > show #3/M target c > show #3/L target c > show #3/K target c > show #1/J target c > hide #1/J target abp > hide #1/M target abp > hide #1/R target abp > hide #1/S target abp > hide #1/T target abp > hide #1/U target abp > hide #1/V target abp > hide #1/W target abp > hide #1/X target abp > hide #1/Y target abp > hide #2/A target abp > hide #3/J target abp > hide #2/A target abp > show #2/A target abp > show #3/J target abp > hide #3/A target abp > hide #3/B target abp > hide #3/C target abp > hide #3/D target abp > hide #3/E target abp > hide #3/F target abp > hide #3/G target abp > hide #3/H target abp > hide #3/K target abp > hide #3/L target abp > show #3/A target c > show #3/B target c > show #3/C target c > show #3/D target c > show #3/E target c > show #3/F target c > show #3/G target c > show #3/H target c > show #3/I target c > show #3/L target c > show #3/M target c > show #3/N target c > show #3/O target c > show #3/Q target c > style selAtoms stick Changed 24648 atom styles > nucleotides selAtoms tube/slab shape ellipsoid > style selAtoms stick Changed 24648 atom styles > style selAtoms ball Changed 24648 atom styles > style selAtoms ball Changed 24648 atom styles > select clear > style selAtoms stick Changed 82027 atom styles > style selAtoms sphere Changed 82027 atom styles > style selAtoms stick Changed 82027 atom styles > style selAtoms ball Changed 82027 atom styles > style selAtoms sphere Changed 82027 atom styles > preset "initial styles" cartoon Preset implemented in Python; no expansion to individual ChimeraX commands available. > color selAtoms bychain > hide #!1.3 models > hide #!1.2 models > hide #1/Z target c > hide #1/M target c > hide #1/S target c > hide #1/T target c > hide #1/U target c > hide #1/V target c > hide #1/V target c > hide #1/W target c > hide #1/X target c > hide #1/Y target c > hide #1/R target c > hide #!1.1 models > hide #1/M target abp > hide #1/R target abp > hide #1/S target abp > hide #1/T target abp > hide #1/S target abp > hide #1/U target abp > hide #1/V target abp > hide #1/W target abp > hide #1/X target abp > hide #3/R target abp > hide #3/J target abp > hide #3/Q target abp > hide #3/P target abp > hide #1/X target abp > hide #1/Y target abp > hide #1/W target abp > show #2/A target s > select #1 43702 atoms, 44998 bonds, 425 pseudobonds, 3 models selected > ui mousemode rightMode "translate selected models" > ~select #1 Nothing selected > select #3 24648 atoms, 26356 bonds, 731 pseudobonds, 1 model selected > ui mousemode rightMode "translate selected models" > select clear > ui mousemode rightMode "rotate selected models" > select #1 43702 atoms, 44998 bonds, 425 pseudobonds, 3 models selected > ui mousemode rightMode "rotate selected models" > select #3 24648 atoms, 26356 bonds, 731 pseudobonds, 1 model selected > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "translate selected models" > select #1 43702 atoms, 44998 bonds, 425 pseudobonds, 3 models selected > ui mousemode rightMode "rotate selected models" > select #3 24648 atoms, 26356 bonds, 731 pseudobonds, 1 model selected > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > select clear > ui mousemode rightMode "translate selected models" > select #1 43702 atoms, 44998 bonds, 425 pseudobonds, 3 models selected > select #2.1 5 pseudobonds, 1 model selected > select #2 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > ui mousemode rightMode "translate selected models" > ~select #2 Nothing selected > select #2 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > ui mousemode rightMode "translate selected models" > lighting full > lighting soft > lighting simple > lighting simple > lighting soft > lighting full > lighting full > lighting soft > ui mousemode rightMode "translate selected models" > ~select #2 Nothing selected > select #2 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > ui mousemode rightMode "translate selected models" > select #3 24648 atoms, 26356 bonds, 731 pseudobonds, 1 model selected > ui mousemode rightMode "translate selected models" > ~select #3 Nothing selected > color #2/A #fd6666 target s > hide #2/A target abp > hide #2/A target c > color #3/B #b3b3b3 target c > color #3/B #ffff0a target c > rainbow #2 structures palette pastel2-4 Unknown command: chain #1 structures palette pastel2-4 Unknown command: bychain #1 structures palette pastel2-4 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > set silhouetteDepthJump 0.02 > color modify /2 whiteness - 50 > color modify /3 whiteness - 50 > color modify /1 whiteness - 50 > rainbow #1 structures palette pastel2-4 > color selAtoms bychain > toolshed show "Marker Placement" > color #3/K #b3b3b3 target c Fetching compressed palette 130451 from http://www.colourlovers.com/api/palette/130451?format=json > rainbow chains palette 130451 Unknown command: palette pastel2-4 > rainbow #1 chains palette paired-6 Fetching compressed palette palette from http://www.colourlovers.com/api/palettes?keywords=palette&format=json&numResults=100 Could not find palette palette at COLOURlovers.com using keyword search Could not find palette palette at COLOURlovers.com using keyword search Could not find palette palette at COLOURlovers.com using keyword search Could not find palette palette at COLOURlovers.com using keyword search Could not find palette palette at COLOURlovers.com using keyword search Fetching compressed palette let them eat cakeby lunalein from http://www.colourlovers.com/api/palettes?keywords=let%20them%20eat%20cakeby%20lunalein&format=json&numResults=100 Could not find palette let them eat cakeby lunalein at COLOURlovers.com using keyword search Fetching compressed palette let from http://www.colourlovers.com/api/palettes?keywords=let&format=json&numResults=100 Could not find palette let at COLOURlovers.com using keyword search Fetching compressed palette Giant Goldfish from http://www.colourlovers.com/api/palettes?keywords=Giant%20Goldfish&format=json&numResults=100 Found 5 ColourLover palettes with name "Giant Goldfish", using palette id 92095 by author manekineko with most views (1011665). To choose a different one use "name by author" or id number. > rainbow #1 chains palette Giant Goldfish Fetching compressed palette (???) from http://www.colourlovers.com/api/palettes?keywords=%28%3F%3F%3F%29&format=json&numResults=100 Could not find palette (???) at COLOURlovers.com using keyword search Fetching compressed palette Thought Provoking from http://www.colourlovers.com/api/palettes?keywords=Thought%20Provoking&format=json&numResults=100 Found 9 ColourLover palettes with name "Thought Provoking", using palette id 694737 by author Miss_Anthropy with most views (428485). To choose a different one use "name by author" or id number. > rainbow #1 chains palette Thought Provoking Fetching compressed palette Melon Ball Surprise from http://www.colourlovers.com/api/palettes?keywords=Melon%20Ball%20Surprise&format=json&numResults=100 Found 2 ColourLover palettes with name "Melon Ball Surprise", using palette id 3432864 by author MistyAamen with most views (60). To choose a different one use "name by author" or id number. > rainbow #1 chains palette Melon Ball Surprise Fetching compressed palette Good Friends from http://www.colourlovers.com/api/palettes?keywords=Good%20Friends&format=json&numResults=100 Found 10 ColourLover palettes with name "Good Friends", using palette id 77121 by author Yasmino with most views (231348). To choose a different one use "name by author" or id number. > rainbow #3 chains palette Good Friends Fetching compressed palette forever lost from http://www.colourlovers.com/api/palettes?keywords=forever%20lost&format=json&numResults=100 Found 4 ColourLover palettes with name "forever lost", using palette id 944213 by author agia with most views (76504). To choose a different one use "name by author" or id number. > rainbow #3 chains palette forever lost Fetching compressed palette Wasabi Suicide from http://www.colourlovers.com/api/palettes?keywords=Wasabi%20Suicide&format=json&numResults=100 Found 2 ColourLover palettes with name "Wasabi Suicide", using palette id 482416 by author Miaka with most views (80567). To choose a different one use "name by author" or id number. > rainbow #3 chains palette Wasabi Suicide Fetching compressed palette 1001 Stories from http://www.colourlovers.com/api/palettes?keywords=1001%20Stories&format=json&numResults=100 > rainbow #3 chains palette 1001 Stories Fetching compressed palette Peach Blossoms from http://www.colourlovers.com/api/palettes?keywords=Peach%20Blossoms&format=json&numResults=100 Found 4 ColourLover palettes with name "Peach Blossoms", using palette id 69953 by author XINJUSTX with most views (316). To choose a different one use "name by author" or id number. > rainbow #3 chains palette Peach Blossoms Fetching compressed palette i n v i s i b l e from http://www.colourlovers.com/api/palettes?keywords=i%20n%20v%20i%20s%20i%20b%20l%20e&format=json&numResults=100 Found 3 ColourLover palettes with name "i n v i s i b l e", using palette id 670816 by author tvr with most views (38140). To choose a different one use "name by author" or id number. > rainbow #3 chains palette i n v i s i b l e Fetching compressed palette Japanese Bath from http://www.colourlovers.com/api/palettes?keywords=Japanese%20Bath&format=json&numResults=100 > rainbow #3 chains palette Japanese Bath Fetching compressed palette 400 from http://www.colourlovers.com/api/palette/400?format=json > rainbow #3 chains palette 400 > select #3 24648 atoms, 26356 bonds, 731 pseudobonds, 1 model selected > ui mousemode rightMode "rotate selected models" > select clear > select #3 24648 atoms, 26356 bonds, 731 pseudobonds, 1 model selected > ui mousemode rightMode "translate selected models" > select clear > select #3 24648 atoms, 26356 bonds, 731 pseudobonds, 1 model selected > select clear > select #3 24648 atoms, 26356 bonds, 731 pseudobonds, 1 model selected > ui mousemode rightMode "rotate selected models" > select clear Fetching compressed palette Kami no ke from http://www.colourlovers.com/api/palettes?keywords=Kami%20no%20ke&format=json&numResults=100 > rainbow #3 chains palette Kami no ke Fetching compressed palette Cool Eve from http://www.colourlovers.com/api/palettes?keywords=Cool%20Eve&format=json&numResults=100 > rainbow #3 chains palette Cool Eve Fetching compressed palette f r a g i l e from http://www.colourlovers.com/api/palettes?keywords=f%20r%20a%20g%20i%20l%20e&format=json&numResults=100 Found 10 ColourLover palettes with name "f r a g i l e", using palette id 2367592 by author Tzadkiel with most views (22324). To choose a different one use "name by author" or id number. > rainbow #3 chains palette f r a g i l e Fetching compressed palette Blown Entrepreneur from http://www.colourlovers.com/api/palettes?keywords=Blown%20Entrepreneur&format=json&numResults=100 > rainbow #3 chains palette Blown Entrepreneur > rainbow #1 chains palette Blown Entrepreneur > nucleotides selAtoms tube/slab shape ellipsoid > rainbow #1/I chains palette Blown Entrepreneur Fetching compressed palette Love to All Lovers from http://www.colourlovers.com/api/palettes?keywords=Love%20to%20All%20Lovers&format=json&numResults=100 Could not find palette Love to All Lovers at COLOURlovers.com using keyword search Fetching compressed palette VITAE from http://www.colourlovers.com/api/palettes?keywords=VITAE&format=json&numResults=100 Could not find palette VITAE at COLOURlovers.com using keyword search Fetching compressed palette LoversInJapan from http://www.colourlovers.com/api/palettes?keywords=LoversInJapan&format=json&numResults=100 Found 3 ColourLover palettes with name "LoversInJapan", using palette id 867235 by author lovelyrita with most views (166097). To choose a different one use "name by author" or id number. > rainbow #1/J chains palette LoversInJapan Fetching compressed palette Compatible from http://www.colourlovers.com/api/palettes?keywords=Compatible&format=json&numResults=100 Found 9 ColourLover palettes with name "Compatible", using palette id 932683 by author joy_of_summer with most views (227611). To choose a different one use "name by author" or id number. > rainbow #1/J chains palette Compatible Fetching compressed palette Curiosity Killed from http://www.colourlovers.com/api/palettes?keywords=Curiosity%20Killed&format=json&numResults=100 Found 3 ColourLover palettes with name "Curiosity Killed", using palette id 444487 by author Miaka with most views (144226). To choose a different one use "name by author" or id number. > rainbow #1/J chains palette Curiosity Killed > select #2/A 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > color #2/A #fc0280 target s > color #2/A #fd6666 target s > select clear > save session "/Users/aiste/Desktop/chromosome and Spt6.cxs" > save /Users/aiste/Desktop/image11.png supersample 3 > open 2b8k 2b8k title: 12-subunit RNA Polymerase II [more info...] Chain information for 2b8k #4 --- Chain | Description A | DNA-directed RNA polymerase II largest subunit B | DNA-directed RNA polymerase II 140 kDa polypeptide C | DNA-directed RNA polymerase II 45 kDa polypeptide D | DNA-directed RNA polymerase II 32 kDa polypeptide E | DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide F | DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide G | DNA-directed RNA polymerase II 19 kDa polypeptide H | DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide I | DNA-directed RNA polymerase II subunit 9 J | DNA-directed RNA polymerases I/II/III subunit 10 K | DNA-directed RNA polymerase II 13.6 kDa polypeptide L | DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide Non-standard residues in 2b8k #4 --- ZN — zinc ion > view cofr false > select #4 31040 atoms, 31595 bonds, 34 pseudobonds, 2 models selected > ui mousemode rightMode "translate selected models" > ~select #4 Nothing selected > select #4 31040 atoms, 31595 bonds, 34 pseudobonds, 2 models selected > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "rotate selected models" > ~select #4 Nothing selected > select #4 31040 atoms, 31595 bonds, 34 pseudobonds, 2 models selected > ui mousemode rightMode "rotate selected models" > close #4 > open 2b8k 2b8k title: 12-subunit RNA Polymerase II [more info...] Chain information for 2b8k #4 --- Chain | Description A | DNA-directed RNA polymerase II largest subunit B | DNA-directed RNA polymerase II 140 kDa polypeptide C | DNA-directed RNA polymerase II 45 kDa polypeptide D | DNA-directed RNA polymerase II 32 kDa polypeptide E | DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide F | DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide G | DNA-directed RNA polymerase II 19 kDa polypeptide H | DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide I | DNA-directed RNA polymerase II subunit 9 J | DNA-directed RNA polymerases I/II/III subunit 10 K | DNA-directed RNA polymerase II 13.6 kDa polypeptide L | DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide Non-standard residues in 2b8k #4 --- ZN — zinc ion > select #4 31040 atoms, 31595 bonds, 34 pseudobonds, 2 models selected > ui mousemode rightMode "translate selected models" > select clear > show #4/L target s > show #4/K target s > show #4/J target s > show #4/I target s > show #4/H target s > show #4/F target s > show #4/E target s > show #4/D target s > show #4/C target s > show #4/B target s > show #4/A target s > show #4/L target s > show #4/K target s > show #4/J target s > show #4/I target s > show #4/I target s > show #4/H target s > show #4/G target s > show #4/F target s > show #4/L target c > show #4/K target c > show #4/J target c > show #4/H target c > show #4/G target c > show #4/E target c > show #4/D target c > show #4/C target c > show #4/B target c > show #4/A target c Expected ',' or a keyword > transparency 82 surfaces > hide #4/L target abp > hide #4/K target abp > hide #4/J target abp > hide #4/I target abp > hide #4/H target abp > hide #4/G target abp > hide #4/F target abp > hide #4/E target abp > hide #4/D target abp > hide #4/C target abp > hide #4/B target abp > hide #4/A target abp > show #2/A target abp > show #2/A target abp > hide #2/A target abp > show #2/A target c > hide #2/A target c > show #2/A target s Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > show #2 surfaces Expected ',' or a keyword > ui mousemode rightMode "contour level" > transparency 70 surfaces > transparency 50 surfaces > select #4 31040 atoms, 31595 bonds, 34 pseudobonds, 2 models selected > ui mousemode rightMode "translate selected models" > select clear Fetching compressed palette Strawberry Mousse from http://www.colourlovers.com/api/palettes?keywords=Strawberry%20Mousse&format=json&numResults=100 Found 17 ColourLover palettes with name "Strawberry Mousse", using palette id 533141 by author InDreamsMaybe with most views (314). To choose a different one use "name by author" or id number. > rainbow #4 chains palette Strawberry Mousse Fetching compressed palette 1001 from http://www.colourlovers.com/api/palette/1001?format=json > rainbow #4 chains palette 1001 > transparency 50 surfaces > transparency 30 surfaces > transparency 40 surfaces > transparency 0 surfaces Expected a keyword Fetching compressed palette A Dream in Color from http://www.colourlovers.com/api/palettes?keywords=A%20Dream%20in%20Color&format=json&numResults=100 > rainbow #2 chains palette A Dream in Color > volume selMaps style mesh No volumes specified No volumes specified Fetching compressed palette t r a n c e from http://www.colourlovers.com/api/palettes?keywords=t%20r%20a%20n%20c%20e&format=json&numResults=100 Found 3 ColourLover palettes with name "t r a n c e", using palette id 594151 by author electroluv with most views (66565). To choose a different one use "name by author" or id number. > rainbow #2 chains palette t r a n c e Fetching compressed palette Thumbelina from http://www.colourlovers.com/api/palettes?keywords=Thumbelina&format=json&numResults=100 Found 28 ColourLover palettes with name "Thumbelina", using palette id 634148 by author angelafaye with most views (34782). To choose a different one use "name by author" or id number. > rainbow #2 chains palette Thumbelina Fetching compressed palette Sweet Lolly from http://www.colourlovers.com/api/palettes?keywords=Sweet%20Lolly&format=json&numResults=100 > rainbow #2 chains palette Sweet Lolly Fetching compressed palette My pet elephant from http://www.colourlovers.com/api/palettes?keywords=My%20pet%20elephant&format=json&numResults=100 > rainbow #2 chains palette My pet elephant Fetching compressed palette Classical from http://www.colourlovers.com/api/palettes?keywords=Classical&format=json&numResults=100 > rainbow #2 chains palette Classical Fetching compressed palette [Chic] - Mellow from http://www.colourlovers.com/api/palettes?keywords=%5BChic%5D%20-%20Mellow&format=json&numResults=100 > rainbow #2 chains palette [Chic] - Mellow Fetching compressed palette nightgown. from http://www.colourlovers.com/api/palettes?keywords=nightgown.&format=json&numResults=100 > rainbow #2 chains palette nightgown. Fetching compressed palette Serenity is . . . from http://www.colourlovers.com/api/palettes?keywords=Serenity%20is%20.%20.%20.&format=json&numResults=100 Could not find palette Serenity is . . . at COLOURlovers.com using keyword search Could not find palette Love to All Lovers at COLOURlovers.com using keyword search Fetching compressed palette If We Should Meet from http://www.colourlovers.com/api/palettes?keywords=If%20We%20Should%20Meet&format=json&numResults=100 > rainbow #2 chains palette If We Should Meet Fetching compressed palette Still Here from http://www.colourlovers.com/api/palettes?keywords=Still%20Here&format=json&numResults=100 Found 10 ColourLover palettes with name "Still Here", using palette id 1564528 by author faith4faith with most views (5186). To choose a different one use "name by author" or id number. > rainbow #2 chains palette Still Here Fetching compressed palette shattered silence from http://www.colourlovers.com/api/palettes?keywords=shattered%20silence&format=json&numResults=100 > rainbow #2 chains palette shattered silence Fetching compressed palette God's Daughter from http://www.colourlovers.com/api/palettes?keywords=God%27s%20Daughter&format=json&numResults=100 > rainbow #2 chains palette God's Daughter > save /Users/aiste/Desktop/image12.png supersample 3 > select #2 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > ui mousemode rightMode "translate selected models" > select clear > select #3 24648 atoms, 26356 bonds, 731 pseudobonds, 1 model selected > ~select #3 Nothing selected > select #4 31040 atoms, 31595 bonds, 34 pseudobonds, 2 models selected > ui mousemode rightMode "translate selected models" > select clear > select #2 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > ui mousemode rightMode "rotate selected models" > select clear > open 6O9L 6o9l title: Human holo-PIC in the closed state [more info...] Chain information for 6o9l #5 --- Chain | Description 0 | TFIIH basal transcription factor complex helicase XPD subunit 1 | General transcription factor IIH subunit 1 2 | General transcription factor IIH subunit 4, p52 3 | CDK-activating kinase assembly factor MAT1 4 | General transcription factor IIH subunit 3 5 | General transcription factor IIH subunit 5 6 | General transcription factor IIH subunit 2 7 | TFIIH basal transcription factor complex helicase XPB subunit 8 | Cyclin-dependent kinase 7 9 | Cyclin-H A | DNA-directed RNA polymerase II subunit RPB1 B | DNA-directed RNA polymerase II subunit RPB2 C | DNA-directed RNA polymerase II subunit RPB3 D | DNA-directed RNA polymerase II subunit RPB4 E | DNA-directed RNA polymerase II subunit RPB5 F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 G | DNA-directed RNA polymerase II subunit RPB7 H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 I | DNA-directed RNA polymerase II subunit RPB9 J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 K | DNA-directed RNA polymerase II subunit RPB11-a L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 M | Transcription initiation factor IIB N | Transcription initiation factor IIA subunit 1 O | Transcription initiation factor IIA subunit 2 P | TATA-box-binding protein Q | General transcription factor IIE subunit 1 R | Transcription initiation factor IIE subunit β S | General transcription factor IIF subunit 1 T | General transcription factor IIF subunit 2 U | Transcription elongation factor A protein 1 X | DNA (65-mer) Y | DNA (65-mer) Non-standard residues in 6o9l #5 --- MG — magnesium ion SF4 — iron/sulfur cluster ZN — zinc ion > hide #5/9 target abp > hide #5/8 target abp > hide #5/7 target abp > hide #5/6 target abp > hide #5/5 target abp > hide #5/A target abp > hide #5/B target abp > hide #5/C target abp > hide #5/D target abp > hide #5/F target abp > hide #5/G target abp > hide #5/H target abp > hide #5/I target abp > hide #5/J target abp > hide #5/K target abp > hide #5/L target abp > hide #5/M target abp > hide #5/O target abp > hide #5/P target abp > hide #5/9 target abp > hide #5/8 target abp > hide #5/7 target abp > hide #5/6 target abp > hide #5/5 target abp > hide #5/4 target abp > hide #5/3 target abp > hide #5/2 target abp > hide #5/1 target abp > hide #5/0 target abp > hide #5/U target abp > hide #5/T target abp > hide #5/S target abp > hide #5/R target abp > hide #5/Q target abp > hide #5/P target abp > select #5 81800 atoms, 83651 bonds, 142 pseudobonds, 3 models selected > ui mousemode rightMode "translate selected models" > select clear > hide #5/E target abp > hide #5/N target abp > select #5 81800 atoms, 83651 bonds, 142 pseudobonds, 3 models selected > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > select clear > select #5 81800 atoms, 83651 bonds, 142 pseudobonds, 3 models selected > show #5/X target c > show #5/Y target c > nucleotides selAtoms tube/slab shape ellipsoid > select #4 31040 atoms, 31595 bonds, 34 pseudobonds, 2 models selected > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > select clear > select #2 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > ui mousemode rightMode "translate selected models" > select clear > select #4 31040 atoms, 31595 bonds, 34 pseudobonds, 2 models selected > ui mousemode rightMode "translate selected models" > select clear > select #1 43702 atoms, 44998 bonds, 425 pseudobonds, 3 models selected > ui mousemode rightMode "rotate selected models" > select clear > rainbow #4/Y chains palette Blown Entrepreneur > rainbow #5/Y chains palette Blown Entrepreneur > rainbow #5/Y chains palette My pet elephant Fetching compressed palette The First Raindrop from http://www.colourlovers.com/api/palettes?keywords=The%20First%20Raindrop&format=json&numResults=100 Could not find palette The First Raindrop at COLOURlovers.com using keyword search > rainbow #5/Y chains palette Blown Entrepreneur Fetching compressed palette Aviation from http://www.colourlovers.com/api/palettes?keywords=Aviation&format=json&numResults=100 Found 7 ColourLover palettes with name "Aviation", using palette id 1577314 by author Capricciosa with most views (212). To choose a different one use "name by author" or id number. > rainbow #5/Y chains palette Aviation Fetching compressed palette devastating loss from http://www.colourlovers.com/api/palettes?keywords=devastating%20loss&format=json&numResults=100 Could not find palette devastating loss at COLOURlovers.com using keyword search Fetching compressed palette More About Money from http://www.colourlovers.com/api/palettes?keywords=More%20About%20Money&format=json&numResults=100 Could not find palette More About Money at COLOURlovers.com using keyword search Fetching compressed palette threadless from http://www.colourlovers.com/api/palettes?keywords=threadless&format=json&numResults=100 Found 4 ColourLover palettes with name "threadless", using palette id 27905 by author COLOURlover with most views (135079). To choose a different one use "name by author" or id number. > rainbow #5/Y,X chains palette threadless Could not find palette Serenity is . . . at COLOURlovers.com using keyword search > rainbow #5/Y,X chains palette Blown Entrepreneur Could not find palette Love to All Lovers at COLOURlovers.com using keyword search Fetching compressed palette teal brocade from http://www.colourlovers.com/api/palettes?keywords=teal%20brocade&format=json&numResults=100 > rainbow #5/Y,X chains palette teal brocade Could not find palette devastating loss at COLOURlovers.com using keyword search Could not find palette More About Money at COLOURlovers.com using keyword search Fetching compressed palette Dutch Seas from http://www.colourlovers.com/api/palettes?keywords=Dutch%20Seas&format=json&numResults=100 > rainbow #5/Y,X chains palette Dutch Seas Fetching compressed palette Loyal Friends from http://www.colourlovers.com/api/palettes?keywords=Loyal%20Friends&format=json&numResults=100 Could not find palette Loyal Friends at COLOURlovers.com using keyword search Fetching compressed palette November from http://www.colourlovers.com/api/palettes?keywords=November&format=json&numResults=100 Found 4 ColourLover palettes with name "November", using palette id 1463444 by author ChairmanCao with most views (15593). To choose a different one use "name by author" or id number. > rainbow #5/Y,X chains palette November Fetching compressed palette Spring Rain from http://www.colourlovers.com/api/palettes?keywords=Spring%20Rain&format=json&numResults=100 Found 18 ColourLover palettes with name "Spring Rain", using palette id 112096 by author Steph6 with most views (9746). To choose a different one use "name by author" or id number. > rainbow #5/Y,X chains palette Spring Rain Fetching compressed palette Milk,Apple&Sky from http://www.colourlovers.com/api/palettes?keywords=Milk%2CApple%26Sky&format=json&numResults=100 > rainbow #5/Y,X chains palette Milk,Apple&Sky > select #2 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > ui mousemode rightMode "translate selected models" > select clear Fetching compressed palette Indie Lemon from http://www.colourlovers.com/api/palettes?keywords=Indie%20Lemon&format=json&numResults=100 > rainbow #5/X chains palette Indie Lemon Fetching compressed palette IGentle Waves from http://www.colourlovers.com/api/palettes?keywords=IGentle%20Waves&format=json&numResults=100 Could not find palette IGentle Waves at COLOURlovers.com using keyword search Fetching compressed palette Gentle Waves from http://www.colourlovers.com/api/palettes?keywords=Gentle%20Waves&format=json&numResults=100 Found 6 ColourLover palettes with name "Gentle Waves", using palette id 2336049 by author Tzadkiel with most views (360). To choose a different one use "name by author" or id number. > rainbow #5/X chains palette Gentle Waves Fetching compressed palette An Old Friend from http://www.colourlovers.com/api/palettes?keywords=An%20Old%20Friend&format=json&numResults=100 Found 11 ColourLover palettes with name "An Old Friend", using palette id 919419 by author joy_of_summer with most views (47553). To choose a different one use "name by author" or id number. > rainbow #5/X chains palette An Old Friend Fetching compressed palette 400 unique artists ? from http://www.colourlovers.com/api/palettes?keywords=400%20unique%20artists%20%3F&format=json&numResults=100 > rainbow #5/X chains palette 400 unique artists ? Fetching compressed palette A Kiss To Awake from http://www.colourlovers.com/api/palettes?keywords=A%20Kiss%20To%20Awake&format=json&numResults=100 > rainbow #5/X chains palette A Kiss To Awake > select #1/I:-77 19 atoms, 20 bonds selected Missing or invalid "atoms" argument: invalid atoms specifier Expected fewer arguments > delete sel > select #1/J:77 22 atoms, 24 bonds selected > select #1/I:-76 22 atoms, 24 bonds selected > delete sel > delete sel > delete sel > open 3psi 3psi title: Crystal Structure of the Spt6 core domain from Saccharomyces cerevisiae, Form Spt6(239-1451) [more info...] Chain information for 3psi #6 --- Chain | Description A | Transcription elongation factor SPT6 > hide #!6.1 models > select #6 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "rotate selected models" > show #6/A target s > ui mousemode rightMode "translate selected models" > select #2 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > ui mousemode rightMode "translate selected models" > select clear > select #6.1 5 pseudobonds, 1 model selected > select #6 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > ui mousemode rightMode "translate selected models" > select clear > open 3psi 3psi title: Crystal Structure of the Spt6 core domain from Saccharomyces cerevisiae, Form Spt6(239-1451) [more info...] Chain information for 3psi #7 --- Chain | Description A | Transcription elongation factor SPT6 > hide #!7.1 models > select #7 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > show #7/A target s > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > select clear > select #2 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > select clear > select #6 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > ui mousemode rightMode "translate selected models" > select clear > color #7/A #e6e6e6 target s > color #2/A #cccccc target s > color #2/A #999999 target s > color #2/A #e6e6e6 target s > select #6.1 5 pseudobonds, 1 model selected > select #6 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > select clear > color #6/A #408002 target s > color #6/A #108040 target s Found 3 ColourLover palettes with name "Curiosity Killed", using palette id 444487 by author Miaka with most views (144226). To choose a different one use "name by author" or id number. > rainbow #2 chains palette Curiosity Killed Expected one of 'chains', 'polymers', 'residues', or 'structures' or a keyword Found 3 ColourLover palettes with name "Curiosity Killed", using palette id 444487 by author Miaka with most views (144226). To choose a different one use "name by author" or id number. > rainbow #7 chains palette Curiosity Killed Found 11 ColourLover palettes with name "An Old Friend", using palette id 919419 by author joy_of_summer with most views (47553). To choose a different one use "name by author" or id number. > rainbow #7 chains palette An Old Friend > rainbow #7 chains palette A Kiss To Awake > rainbow #2 chains palette A Kiss To Awake > select clear > select #7 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > ui mousemode rightMode "rotate selected models" > select clear > save /Users/aiste/Desktop/image13.png supersample 3 > select #2 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > ui mousemode rightMode "translate selected models" > select clear > open 2KE8 Summary of feedback from opening 2KE8 fetched from pdb --- warnings | Atom HO5' is not in the residue template for DT #1 in chain A Atom HO5' is not in the residue template for DT #18 in chain B 2ke8 title: NMR solution structure of metal-modified DNA [more info...] Chain information for 2ke8 --- Chain | Description 8.1/A 8.2/A 8.3/A 8.4/A 8.5/A 8.6/A 8.7/A 8.8/A 8.9/A 8.10/A 8.11/A 8.12/A 8.13/A 8.14/A 8.15/A 8.16/A 8.17/A 8.18/A 8.19/A 8.20/A 8.1/B 8.2/B 8.3/B 8.4/B 8.5/B 8.6/B 8.7/B 8.8/B 8.9/B 8.10/B 8.11/B 8.12/B 8.13/B 8.14/B 8.15/B 8.16/B 8.17/B 8.18/B 8.19/B 8.20/B | DNA (5'-D(*TP*TP*ap*ap*TP*TP*TP*(D33)P*(D33)P*(D33)P*ap*ap*ap*TP*TP*ap*A)-3') > select #8 21060 atoms, 22600 bonds, 680 pseudobonds, 41 models selected > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "translate selected models" > select #4 31040 atoms, 31595 bonds, 34 pseudobonds, 2 models selected > ui mousemode rightMode "translate selected models" > select #8 21060 atoms, 22600 bonds, 680 pseudobonds, 41 models selected > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "rotate selected models" > nucleotides selAtoms tube/slab shape ellipsoid > close #8 > open 6DNV Summary of feedback from opening 6DNV fetched from pdb --- note | Fetching compressed mmCIF 6dnv from http://files.rcsb.org/download/6dnv.cif 6dnv title: Crystal Structure of Neisseria meningitidis DsbD n-terminal domain in the reduced form [more info...] Chain information for 6dnv #8 --- Chain | Description A B | Thiol:disulfide interchange protein DsbD Non-standard residues in 6dnv #8 --- SO4 — sulfate ion 6dnv mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > close #8 > open 5ZLD Summary of feedback from opening 5ZLD fetched from pdb --- warnings | Atom HO5' is not in the residue template for DC #1 in chain A Atom HO5' is not in the residue template for DC #15 in chain B note | Fetching compressed mmCIF 5zld from http://files.rcsb.org/download/5zld.cif 5zld title: Solution NMR structure of A 14-mer double stranded DNA duplex cgcgaaatttcgcg [more info...] Chain information for 5zld --- Chain | Description 8.1/A 8.2/A 8.3/A 8.4/A 8.1/B 8.2/B 8.3/B 8.4/B | DNA (5'-D(*CP*GP*CP*GP*ap*ap*ap*TP*TP*TP*CP*GP*CP*G)-3') > select #8 3544 atoms, 3816 bonds, 144 pseudobonds, 5 models selected > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > select clear > open 5ZLD Summary of feedback from opening 5ZLD fetched from pdb --- warnings | Atom HO5' is not in the residue template for DC #1 in chain A Atom HO5' is not in the residue template for DC #15 in chain B 5zld title: Solution NMR structure of A 14-mer double stranded DNA duplex cgcgaaatttcgcg [more info...] Chain information for 5zld --- Chain | Description 9.1/A 9.2/A 9.3/A 9.4/A 9.1/B 9.2/B 9.3/B 9.4/B | DNA (5'-D(*CP*GP*CP*GP*ap*ap*ap*TP*TP*TP*CP*GP*CP*G)-3') > select #9.1 886 atoms, 954 bonds, 36 pseudobonds, 2 models selected > select #9 3544 atoms, 3816 bonds, 144 pseudobonds, 5 models selected > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > select clear > select #7 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > ui mousemode rightMode "translate selected models" > nucleotides selAtoms tube/slab shape ellipsoid > select #4 31040 atoms, 31595 bonds, 34 pseudobonds, 2 models selected > ui mousemode rightMode "translate selected models" > select clear > select #7 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > ui mousemode rightMode "translate selected models" > select clear > select #7 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > ui mousemode rightMode "translate selected models" > rainbow #9 chains palette A Kiss To Awake > rainbow #9 chains palette Milk,Apple&Sky > rainbow #8 chains palette Milk,Apple&Sky > select #6 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > select clear > delete sel > select clear > delete sel > select #3/J:-308 22 atoms, 24 bonds selected > delete sel > select #3/I:308 20 atoms, 21 bonds selected > delete sel > select clear > delete sel Exception ignored in: <function Buffer.__del__ at 0x11a3b3950> Traceback (most recent call last): File "/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py", line 2393, in __del__ % self.shader_variable_name) RuntimeError: OpenGL buffer "None" was not deleted before core.graphics.Buffer destroyed > delete sel > delete sel > select clear > delete sel > delete sel > select clear > select clear > delete sel > select #3/J:-307 19 atoms, 20 bonds selected > delete sel > select clear > select #2 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > ui mousemode rightMode "translate selected models" > select clear > delete sel > delete sel > delete sel > delete sel > select #2 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > ui mousemode rightMode "translate selected models" > select clear > select #3 24387 atoms, 26061 bonds, 718 pseudobonds, 2 models selected > ui mousemode rightMode "translate selected models" > select #1 42319 atoms, 43439 bonds, 340 pseudobonds, 3 models selected > ui mousemode rightMode "translate selected models" > select clear > select #3 24387 atoms, 26061 bonds, 718 pseudobonds, 2 models selected Exception ignored in: <function Buffer.__del__ at 0x11a3b3950> Traceback (most recent call last): File "/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py", line 2393, in __del__ % self.shader_variable_name) RuntimeError: OpenGL buffer "None" was not deleted before core.graphics.Buffer destroyed > ui mousemode rightMode "translate selected models" > select clear > select #2 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > select #2 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > ui mousemode rightMode "translate selected models" > select clear > open 5ZLD Summary of feedback from opening 5ZLD fetched from pdb --- warnings | Atom HO5' is not in the residue template for DC #1 in chain A Atom HO5' is not in the residue template for DC #15 in chain B 5zld title: Solution NMR structure of A 14-mer double stranded DNA duplex cgcgaaatttcgcg [more info...] Chain information for 5zld --- Chain | Description 10.1/A 10.2/A 10.3/A 10.4/A 10.1/B 10.2/B 10.3/B 10.4/B | DNA (5'-D(*CP*GP*CP*GP*ap*ap*ap*TP*TP*TP*CP*GP*CP*G)-3') > select #10.1 886 atoms, 954 bonds, 36 pseudobonds, 2 models selected > select #10 3544 atoms, 3816 bonds, 144 pseudobonds, 5 models selected > ui mousemode rightMode "translate selected models" > select clear > nucleotides selAtoms tube/slab shape ellipsoid Fetching compressed palette w o r d l e s s . from http://www.colourlovers.com/api/palettes?keywords=w%20o%20r%20d%20l%20e%20s%20s%20.&format=json&numResults=100 > rainbow #10 chains palette w o r d l e s s . Fetching compressed palette Someone Like Me from http://www.colourlovers.com/api/palettes?keywords=Someone%20Like%20Me&format=json&numResults=100 Found 3 ColourLover palettes with name "Someone Like Me", using palette id 754405 by author munsteri with most views (20645). To choose a different one use "name by author" or id number. > rainbow #10 chains palette Someone Like Me > select #10 3544 atoms, 3816 bonds, 144 pseudobonds, 5 models selected > ui mousemode rightMode "translate selected models" > select clear > ui mousemode rightMode "rotate selected models" > select #10 3544 atoms, 3816 bonds, 144 pseudobonds, 5 models selected > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > select clear > ui mousemode rightMode "translate selected models" > select #10 3544 atoms, 3816 bonds, 144 pseudobonds, 5 models selected > ui mousemode rightMode "translate selected models" > select clear > open 5ZLD Summary of feedback from opening 5ZLD fetched from pdb --- warnings | Atom HO5' is not in the residue template for DC #1 in chain A Atom HO5' is not in the residue template for DC #15 in chain B 5zld title: Solution NMR structure of A 14-mer double stranded DNA duplex cgcgaaatttcgcg [more info...] Chain information for 5zld --- Chain | Description 11.1/A 11.2/A 11.3/A 11.4/A 11.1/B 11.2/B 11.3/B 11.4/B | DNA (5'-D(*CP*GP*CP*GP*ap*ap*ap*TP*TP*TP*CP*GP*CP*G)-3') > select #11 3544 atoms, 3816 bonds, 144 pseudobonds, 5 models selected > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > select clear > nucleotides selAtoms tube/slab shape ellipsoid > rainbow #10 chains palette Milk,Apple&Sky > rainbow #11 chains palette Milk,Apple&Sky Found 3 ColourLover palettes with name "Someone Like Me", using palette id 754405 by author munsteri with most views (20645). To choose a different one use "name by author" or id number. > rainbow #10 chains palette Someone Like Me > select #6 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > ui mousemode rightMode "translate selected models" > select clear > delete sel > select clear > save /Users/aiste/Desktop/image14.png supersample 3 > lighting simple > lighting soft > lighting full > lighting soft > save /Users/aiste/Desktop/image15.png supersample 3 > save session "/Users/aiste/Desktop/Spt6 binding events.cxs" > select #6 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > select clear > select #9 3544 atoms, 3816 bonds, 144 pseudobonds, 5 models selected > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > select clear > select #8 3544 atoms, 3816 bonds, 144 pseudobonds, 5 models selected > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > select clear > select #7 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > select #2 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > ui mousemode rightMode "translate selected models" > save /Users/aiste/Desktop/image16.png supersample 3 > select #7 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > ui mousemode rightMode "translate selected models" > select #11 3544 atoms, 3816 bonds, 144 pseudobonds, 5 models selected > ui mousemode rightMode "translate selected models" > select clear > select #6 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > ui mousemode rightMode "translate selected models" > select clear > save /Users/aiste/Desktop/image17.png supersample 3 > select #6.1 5 pseudobonds, 1 model selected > select #6 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > ui mousemode rightMode "translate selected models" > select clear > save /Users/aiste/Desktop/image18.png supersample 3 > select clear > delete sel > delete sel > select #2 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > ui mousemode rightMode "translate selected models" > open 6gej 6gej title: Chromatin remodeller-nucleosome complex at 3.6 A resolution. [more info...] Chain information for 6gej #12 --- Chain | Description A B | Histone H3 C D | Histone H4 E F | Histone H2A.1 G H | Histone H2B.1 I | DNA (154-mer) J | DNA (154-mer) M | Helicase SWR1 R | Actin-like protein ARP6 S | Vacuolar protein sorting-associated protein 71 T V X | RuvB-like protein 1 U W Y | RuvB-like protein 2 Z | Vacuolar protein sorting-associated protein 72 Non-standard residues in 6gej #12 --- ADP — adenosine-5'-diphosphate BEF — beryllium trifluoride ion MG — magnesium ion ZN — zinc ion > hide #12/Y target abp > hide #12/W target abp > hide #12/V target abp > hide #12/T target abp > hide #12/S target abp > hide #12/R target abp > hide #12/M target abp > hide #12/Z target abp > hide #12/M target abp > hide #12/R target abp > hide #12/S target abp > hide #12/T target abp > hide #12/U target abp > hide #12/X target abp > hide #!12.3 models > hide #!12.2 models > hide #!12.1 models > select #12 43702 atoms, 44998 bonds, 425 pseudobonds, 3 models selected > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > nucleotides selAtoms tube/slab shape ellipsoid > show #12/I target c > show #12/J target c > select clear > cartoon style #12 6gej #12 \- 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 > hide #12/A target abp > hide #12/B target abp > hide #12/C target abp > show #12/A target c > show #12/B target c > show #12/C target c > show #12/D target c > cartoon style modeHelix tube sides 24 > show #12/C target c > hide #12/C target abp > hide #12/D target abp > hide #12/G target abp > hide #12/H target abp > hide #12/H target abp > show #12/H target c > show #12/E target c > show #12/D target c > show #12/C target c > show #12/B target c > hide #12/B target abp > hide #12/C target abp > hide #12/D target abp > hide #12/E target abp > hide #12/G target abp > hide #12/H target abp > hide #12/F target abp > show #12/F target c > rainbow #11 structures palette Blown Entrepreneur > rainbow #12 structures palette Blown Entrepreneur > rainbow #12 chains palette Blown Entrepreneur > rainbow #12/J chains palette Blown Entrepreneur > select #1 42319 atoms, 43439 bonds, 340 pseudobonds, 3 models selected > ui mousemode rightMode "translate selected models" > select #12 43702 atoms, 44998 bonds, 425 pseudobonds, 3 models selected > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > select clear > select #5 81364 atoms, 83160 bonds, 122 pseudobonds, 3 models selected > ui mousemode rightMode "translate selected models" > select #9 3544 atoms, 3816 bonds, 144 pseudobonds, 5 models selected > ui mousemode rightMode "translate selected models" > select #8 3544 atoms, 3816 bonds, 144 pseudobonds, 5 models selected > ui mousemode rightMode "translate selected models" > select #6 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > ui mousemode rightMode "translate selected models" > select #2 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > ui mousemode rightMode "translate selected models" > select clear > save /Users/aiste/Desktop/image19.png supersample 3 > select #12 43702 atoms, 44998 bonds, 425 pseudobonds, 3 models selected > ui mousemode rightMode "translate selected models" > select #1 42319 atoms, 43439 bonds, 340 pseudobonds, 3 models selected > ui mousemode rightMode "translate selected models" > select clear > select #2 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > ui mousemode rightMode "translate selected models" > select clear > select #2 13677 atoms, 13816 bonds, 5 pseudobonds, 1 model selected > ui mousemode rightMode "translate selected models" > delete sel > select #5 81364 atoms, 83160 bonds, 122 pseudobonds, 3 models selected > ui mousemode rightMode "translate selected models" > select clear > delete sel > delete sel > delete sel Traceback (most recent call last): File "/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/nucleotides/_data.py", line 621, in _rebuild_molecule mol.bounds() # need to recompute ribbon first TODO: another way? File "/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 1670, in bounds self._update_graphics_if_needed() # Ribbon bounds computed from graphics File "/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 321, in _update_graphics_if_needed self._update_ribbon_tethers() File "/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 1655, in _update_ribbon_tethers tp.positions = _tether_placements(xyz1, xyz2, radii, shape) File "/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 3147, in _tether_placements return _bond_cylinder_placements(xyz0, xyz1, radius) File "/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 3072, in _bond_cylinder_placements cylinder_rotations(axyz0, axyz1, radii, p) ValueError: Cylinder end-point and radii arrays must have same size, got 268 267 267 Error processing trigger "changes": Cylinder end-point and radii arrays must have same size, got 268 267 267: ValueError: Cylinder end-point and radii arrays must have same size, got 268 267 267 File "/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 3072, in _bond_cylinder_placements cylinder_rotations(axyz0, axyz1, radii, p) See log for complete Python traceback. Traceback (most recent call last): File "/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 2637, in _update_graphics_if_needed s[i]._update_graphics_if_needed() File "/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 321, in _update_graphics_if_needed self._update_ribbon_tethers() File "/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 1655, in _update_ribbon_tethers tp.positions = _tether_placements(xyz1, xyz2, radii, shape) File "/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 3147, in _tether_placements return _bond_cylinder_placements(xyz0, xyz1, radius) File "/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 3072, in _bond_cylinder_placements cylinder_rotations(axyz0, axyz1, radii, p) ValueError: Cylinder end-point and radii arrays must have same size, got 268 267 267 Error processing trigger "graphics update": Cylinder end-point and radii arrays must have same size, got 268 267 267: ValueError: Cylinder end-point and radii arrays must have same size, got 268 267 267 File "/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 3072, in _bond_cylinder_placements cylinder_rotations(axyz0, axyz1, radii, p) See log for complete Python traceback. > select clear > delete sel > select clear > select clear > select clear > delete sel Traceback (most recent call last): File "/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/nucleotides/_data.py", line 621, in _rebuild_molecule mol.bounds() # need to recompute ribbon first TODO: another way? File "/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 1670, in bounds self._update_graphics_if_needed() # Ribbon bounds computed from graphics File "/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 321, in _update_graphics_if_needed self._update_ribbon_tethers() File "/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 1655, in _update_ribbon_tethers tp.positions = _tether_placements(xyz1, xyz2, radii, shape) File "/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 3147, in _tether_placements return _bond_cylinder_placements(xyz0, xyz1, radius) File "/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 3072, in _bond_cylinder_placements cylinder_rotations(axyz0, axyz1, radii, p) ValueError: Cylinder end-point and radii arrays must have same size, got 268 267 267 Error processing trigger "changes": Cylinder end-point and radii arrays must have same size, got 268 267 267: ValueError: Cylinder end-point and radii arrays must have same size, got 268 267 267 File "/Applications/ChimeraX-0.9-rc-2019.06.01.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/structure.py", line 3072, in _bond_cylinder_placements cylinder_rotations(axyz0, axyz1, radii, p) See log for complete Python traceback. OpenGL version: 4.1 ATI-2.8.38 OpenGL renderer: AMD Radeon HD - FirePro D700 OpenGL Engine OpenGL vendor: ATI Technologies Inc.
Change History (3)
comment:1 by , 6 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Bond drawing: cylinder and endpoint arrays differ in size |
comment:2 by , 6 years ago
| Cc: | added |
|---|---|
| Owner: | changed from to |
| Summary: | Bond drawing: cylinder and endpoint arrays differ in size → Nucleotides tethers: Bond drawing: cylinder and endpoint arrays differ in size |
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Appears atoms were deleted and then error is in nucleotides _rebuild_molecule() routine and _tether_placements() code.