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Opened 7 years ago
Closed 7 years ago
#1730 closed defect (duplicate)
self._positions is None
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | 0.9 |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Darwin-18.2.0-x86_64-i386-64bit ChimeraX Version: 0.9 (2018-12-20) Description (Describe the actions that caused this problem to occur here) Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 0.9 (2018-12-20) How to cite UCSF ChimeraX Updating list of available bundles failed: 'list' object has no attribute 'split' > open /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_utp.pdb Summary of feedback from opening /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_utp.pdb --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 3723 messages similar to the above omitted Chain information for c5_utp.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E I | No description available F | No description available G | No description available H | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available X | No description available Y | No description available Z | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_ribo.pdb Chain information for c5_ribo.pdb #2 --- Chain | Description 1 | No description available 2 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N d | No description available O | No description available P | No description available Q | No description available R S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available e g | No description available f | No description available h | No description available i | No description available j m | No description available k | No description available l | No description available n | No description available o | No description available p | No description available > open /Users/lijuanyin/project/kre33_90S/job028_class3d_job026_8c/c5_and_c146ofc2/second_refine/post_2/postprocess_masked.mrc Summary of feedback from opening /Users/lijuanyin/project/kre33_90S/job028_class3d_job026_8c/c5_and_c146ofc2/second_refine/post_2/postprocess_masked.mrc --- notes | vol ignore padd value None m stats None -0.22822514176368713 0.3320360779762268 Opened postprocess_masked.mrc, grid size 480,480,480, pixel 1.08, shown at level 0.0347, step 2, values float32 > open /Users/lijuanyin/project/kre33_90S/figures/for_ed/kre33_map.mrc Summary of feedback from opening /Users/lijuanyin/project/kre33_90S/figures/for_ed/kre33_map.mrc --- notes | vol ignore padd value None m stats None -0.14686203002929688 0.253886878490448 Opened kre33_map.mrc, grid size 480,480,480, pixel 1.08, shown at level -2.76e-05, step 2, values float32 > open /Users/lijuanyin/project/kre33_90S/figures/figure2/emg1_map.mrc Summary of feedback from opening /Users/lijuanyin/project/kre33_90S/figures/figure2/emg1_map.mrc --- notes | vol ignore padd value None m stats None -0.11638116836547852 0.22486688196659088 Opened emg1_map.mrc, grid size 480,480,480, pixel 1.08, shown at level -1.56e-05, step 2, values float32 > open /Users/lijuanyin/project/kre33_90S/figures/figure2/rrp12_map_from_job189.mrc Summary of feedback from opening /Users/lijuanyin/project/kre33_90S/figures/figure2/rrp12_map_from_job189.mrc --- notes | vol ignore padd value None m stats None -0.17061135172843933 0.3109600841999054 Opened rrp12_map_from_job189.mrc, grid size 480,480,480, pixel 1.08, shown at level -3.87e-05, step 2, values float32 > open /Users/lijuanyin/project/kre33_90S/figures/figure2/emg1_complex.pdb Chain information for emg1_complex.pdb #7 --- Chain | Description B | No description available N | No description available O | No description available S | No description available X | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure2/beak2.pdb Chain information for beak2.pdb #8 --- Chain | Description 2 | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure2/rrp12.pdb Chain information for rrp12.pdb #9 --- Chain | Description s | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure2/chainM.pdb Chain information for chainM.pdb #10 --- Chain | Description M | No description available > color #3 light gray > volume #3 transparency 0.5 > volume #3 step 1 level 0.04 > volume #4 step 1 level 0.01 > volume #5 step 1 level 0.04 > volume #6 step 1 level 0.04 > surface dust #1-8 size 5 > set bgColor white > lighting soft > color #1 #2 light gray > color #2/R forest green > color #2/S cyan > color #2/W cornflower blue > color #2/Y hot pink > color #2/Z tomato > hide #1 #2 #7 #8 #9 target a > hide #7 #8 #9 #10 target r > show #2/R /S /W /Z /Y target r > windowsize 600 800 > set silhouettes true > volume #5 #6 hide > color zone #4 near #2 #1 distance 6 > view matrix camera 0.88647,-0.27586,-0.37157,21.602,-0.30963,0.24319,-0.91923,-306,0.34394,0.92993,0.13017,328.02 vol ignore padd value None m stats None -0.2371344417333603 0.35903599858283997 vol ignore padd value None m stats None -0.16461524367332458 0.2752765417098999 > view matrix camera 0.88647,-0.27586,-0.37157,21.602,-0.30963,0.24319,-0.91923,-306,0.34394,0.92993,0.13017,328.02 > save /Users/lijuanyin/project/kre33_90S/figures/for_ed/kre33_position1.png supersample 3 > turn y 70 > save /Users/lijuanyin/project/kre33_90S/figures/for_ed/kre33_position2.png supersample 3 > view matrix camera 0.88647,-0.27586,-0.37157,21.602,-0.30963,0.24319,-0.91923,-306,0.34394,0.92993,0.13017,328.02 > save /Users/lijuanyin/project/kre33_90S/figures/for_ed/kre33_position1.png supersample 3 > turn y 70 > view matrix camera position: -0.045976,-0.27586,-0.9601,-320.95,-0.96969,0.24319,-0.023443,249.46,0.23995,0.92993,-0.27867,83.334 model positions: #1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0,#8,1,0,0,0,0,1,0,0,0,0,1,0,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#9,1,0,0,0,0,1,0,0,0,0,1,0,#10,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix camera -0.045976,-0.27586,-0.9601,-320.95,-0.96969,0.24319,-0.023443,249.46,0.23995,0.92993,-0.27867,83.334 > save /Users/lijuanyin/project/kre33_90S/figures/for_ed/kre33_position2.png supersample 3 > volume #4 hide > hide #1 #2 target r > volume #5 #6 show > color #5 #6 light gray > color #7/X forest green > color #7/B hot pink > color #7/S coral > color #7/N blue violet > color #7/O turquoise > color #9 orange > color #8 yellow > color #10 khaki > color zone #5 near #7 distance 6 > color zone #6 near #7 #8 #9 #10 distance 6 vol ignore padd value None m stats None -0.1281111091375351 0.26489919424057007 vol ignore padd value None m stats None -0.1759013831615448 0.32811522483825684 > view matrix camera 0.88647,-0.27586,-0.37157,21.602,-0.30963,0.24319,-0.91923,-306,0.34394,0.92993,0.13017,328.02 > save /Users/lijuanyin/project/kre33_90S/figures/for_ed/nop14_position1.png supersample 3 > turn y 70 > view matrix camera -0.045976,-0.27586,-0.9601,-320.95,-0.96969,0.24319,-0.023443,249.46,0.23995,0.92993,-0.27867,83.334 > save /Users/lijuanyin/project/kre33_90S/figures/for_ed/nop14_position2.png supersample 3 > view matrix camera 0.88647,-0.27586,-0.37157,21.602,-0.30963,0.24319,-0.91923,-306,0.34394,0.92993,0.13017,328.02 > ui mousemode rightMode zoom Missing required "near" argument > color zone #6 near #9 #10 distance 12 > color zone #6 near #7 #8 #9 #10 distance 20 > surface dust #1-8 size 5 > view matrix camera 0.88647,-0.27586,-0.37157,21.602,-0.30963,0.24319,-0.91923,-306,0.34394,0.92993,0.13017,328.02 > save /Users/lijuanyin/project/kre33_90S/figures/for_ed/nop14_position1.png supersample 3 > view matrix camera position: 0.90725,-0.19704,-0.37157,-16.501,-0.32977,0.21509,-0.91923,-349.08,0.26104,0.95651,0.13017,329.98 model positions: #1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0,#8,1,0,0,0,0,1,0,0,0,0,1,0,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#9,1,0,0,0,0,1,0,0,0,0,1,0,#10,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix camera 0.90725,-0.19704,-0.37157,-16.501,-0.32977,0.21509,-0.91923,-349.08,0.26104,0.95651,0.13017,329.98 > save /Users/lijuanyin/project/kre33_90S/figures/for_ed/nop14_position1.png supersample 3 > turn y 70 > view matrix camera 0.90725,-0.19704,-0.37157,-16.501,-0.32977,0.21509,-0.91923,-349.08,0.26104,0.95651,0.13017,329.98 > turn y 60 > view matrix camera position: 0.13183,-0.19704,-0.97149,-399.77,-0.96096,0.21509,-0.17403,141.95,0.24324,0.95651,-0.16098,142.35 model positions: #1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0,#8,1,0,0,0,0,1,0,0,0,0,1,0,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#9,1,0,0,0,0,1,0,0,0,0,1,0,#10,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix camera 0.13183,-0.19704,-0.97149,-399.77,-0.96096,0.21509,-0.17403,141.95,0.24324,0.95651,-0.16098,142.35 > save /Users/lijuanyin/project/kre33_90S/figures/for_ed/nop14_position2.png supersample 3 > close > open /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_utp.pdb Summary of feedback from opening /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_utp.pdb --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 3723 messages similar to the above omitted Chain information for c5_utp.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E I | No description available F | No description available G | No description available H | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available X | No description available Y | No description available Z | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_ribo.pdb Chain information for c5_ribo.pdb #2 --- Chain | Description 1 | No description available 2 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N d | No description available O | No description available P | No description available Q | No description available R S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available e g | No description available f | No description available h | No description available i | No description available j m | No description available k | No description available l | No description available n | No description available o | No description available p | No description available > open /Users/lijuanyin/project/kre33_90S/job028_class3d_job026_8c/c5_and_c146ofc2/second_refine/post_2/postprocess_masked.mrc Summary of feedback from opening /Users/lijuanyin/project/kre33_90S/job028_class3d_job026_8c/c5_and_c146ofc2/second_refine/post_2/postprocess_masked.mrc --- notes | vol ignore padd value None m stats None -0.22822514176368713 0.3320360779762268 Opened postprocess_masked.mrc, grid size 480,480,480, pixel 1.08, shown at level 0.0347, step 2, values float32 > open /Users/lijuanyin/project/kre33_90S/figures/for_ed/kre33_map.mrc Summary of feedback from opening /Users/lijuanyin/project/kre33_90S/figures/for_ed/kre33_map.mrc --- notes | vol ignore padd value None m stats None -0.14686203002929688 0.253886878490448 Opened kre33_map.mrc, grid size 480,480,480, pixel 1.08, shown at level -2.76e-05, step 2, values float32 > open /Users/lijuanyin/project/kre33_90S/figures/figure2/emg1_map.mrc Summary of feedback from opening /Users/lijuanyin/project/kre33_90S/figures/figure2/emg1_map.mrc --- notes | vol ignore padd value None m stats None -0.11638116836547852 0.22486688196659088 Opened emg1_map.mrc, grid size 480,480,480, pixel 1.08, shown at level -1.56e-05, step 2, values float32 > open /Users/lijuanyin/project/kre33_90S/figures/figure2/rrp12_map_from_job189.mrc Summary of feedback from opening /Users/lijuanyin/project/kre33_90S/figures/figure2/rrp12_map_from_job189.mrc --- notes | vol ignore padd value None m stats None -0.17061135172843933 0.3109600841999054 Opened rrp12_map_from_job189.mrc, grid size 480,480,480, pixel 1.08, shown at level -3.87e-05, step 2, values float32 > open /Users/lijuanyin/project/kre33_90S/figures/figure2/emg1_complex.pdb Chain information for emg1_complex.pdb #7 --- Chain | Description B | No description available N | No description available O | No description available S | No description available X | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure2/beak2.pdb Chain information for beak2.pdb #8 --- Chain | Description 2 | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure2/rrp12.pdb Chain information for rrp12.pdb #9 --- Chain | Description s | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure2/chainM.pdb Chain information for chainM.pdb #10 --- Chain | Description M | No description available > color #3 light gray > volume #3 transparency 0.5 > volume #3 step 1 level 0.04 > volume #4 step 1 level 0.01 > volume #5 step 1 level 0.04 > volume #6 step 1 level 0.04 > surface dust #1-8 size 5 > set bgColor white > lighting soft > color #1 #2 light gray > color #2/R forest green > color #2/S cyan > color #2/W cornflower blue > color #2/Y hot pink > color #2/Z tomato > hide #1 #2 #7 #8 #9 target a > hide #7 #8 #9 #10 target r > show #2/R /S /W /Z /Y target r > windowsize 600 800 > set silhouettes true > volume #5 #6 hide > color zone #4 near #2 #1 distance 6 > view matrix camera 0.88647,-0.27586,-0.37157,21.602,-0.30963,0.24319,-0.91923,-306,0.34394,0.92993,0.13017,328.02 vol ignore padd value None m stats None -0.2371344417333603 0.35903599858283997 vol ignore padd value None m stats None -0.16461524367332458 0.2752765417098999 > windowsize 600 800 > surface dust #1-8 size 5 > view matrix camera 0.90725,-0.19704,-0.37157,-16.501,-0.32977,0.21509,-0.91923,-349.08,0.26104,0.95651,0.13017,329.98 > save /Users/lijuanyin/project/kre33_90S/figures/for_ed/kre33_position1.png supersample 3 > turn y 60 > view matrix camera 0.13183,-0.19704,-0.97149,-399.77,-0.96096,0.21509,-0.17403,141.95,0.24324,0.95651,-0.16098,142.35 > save /Users/lijuanyin/project/kre33_90S/figures/for_ed/kre33_position2.png supersample 3 > show #7 #8 #9 #10 target r > color #7/X forest green > color #7/B hot pink > color #7/S coral > color #7/N blue violet > color #7/O turquoise > color #9 orange > color #8 yellow > color #10 khaki > close > open /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_utp.pdb Summary of feedback from opening /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_utp.pdb --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 3723 messages similar to the above omitted Chain information for c5_utp.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E I | No description available F | No description available G | No description available H | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available X | No description available Y | No description available Z | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_ribo.pdb Chain information for c5_ribo.pdb #2 --- Chain | Description 1 | No description available 2 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N d | No description available O | No description available P | No description available Q | No description available R S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available e g | No description available f | No description available h | No description available i | No description available j m | No description available k | No description available l | No description available n | No description available o | No description available p | No description available > open /Users/lijuanyin/project/kre33_90S/job028_class3d_job026_8c/c5_and_c146ofc2/second_refine/post_2/postprocess_masked.mrc Summary of feedback from opening /Users/lijuanyin/project/kre33_90S/job028_class3d_job026_8c/c5_and_c146ofc2/second_refine/post_2/postprocess_masked.mrc --- notes | vol ignore padd value None m stats None -0.22822514176368713 0.3320360779762268 Opened postprocess_masked.mrc, grid size 480,480,480, pixel 1.08, shown at level 0.0347, step 2, values float32 > open /Users/lijuanyin/project/kre33_90S/figures/for_ed/kre33_map.mrc Summary of feedback from opening /Users/lijuanyin/project/kre33_90S/figures/for_ed/kre33_map.mrc --- notes | vol ignore padd value None m stats None -0.14686203002929688 0.253886878490448 Opened kre33_map.mrc, grid size 480,480,480, pixel 1.08, shown at level -2.76e-05, step 2, values float32 > open /Users/lijuanyin/project/kre33_90S/figures/figure2/emg1_map.mrc Summary of feedback from opening /Users/lijuanyin/project/kre33_90S/figures/figure2/emg1_map.mrc --- notes | vol ignore padd value None m stats None -0.11638116836547852 0.22486688196659088 Opened emg1_map.mrc, grid size 480,480,480, pixel 1.08, shown at level -1.56e-05, step 2, values float32 > open /Users/lijuanyin/project/kre33_90S/figures/figure2/rrp12_map_from_job189.mrc Summary of feedback from opening /Users/lijuanyin/project/kre33_90S/figures/figure2/rrp12_map_from_job189.mrc --- notes | vol ignore padd value None m stats None -0.17061135172843933 0.3109600841999054 Opened rrp12_map_from_job189.mrc, grid size 480,480,480, pixel 1.08, shown at level -3.87e-05, step 2, values float32 > open /Users/lijuanyin/project/kre33_90S/figures/figure2/emg1_complex.pdb Chain information for emg1_complex.pdb #7 --- Chain | Description B | No description available N | No description available O | No description available S | No description available X | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure2/beak2.pdb Chain information for beak2.pdb #8 --- Chain | Description 2 | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure2/rrp12.pdb Chain information for rrp12.pdb #9 --- Chain | Description s | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure2/chainM.pdb Chain information for chainM.pdb #10 --- Chain | Description M | No description available > color #3 #5 #6 light gray > volume #3 transparency 0.5 > volume #3 step 1 level 0.04 > volume #4 step 1 level 0.01 > volume #5 step 1 level 0.04 > volume #6 step 1 level 0.04 > surface dust #1-8 size 5 > set bgColor white > lighting soft > color #1 #2 light gray > color #2/R forest green > color #2/S lime > color #2/W cornflower blue > color #2/Y hot pink > color #2/Z red > hide #1 #2 #7 #8 #9 target a > hide #7 #8 #9 #10 target r > show #2/R /S /W /Z /Y target r > windowsize 600 800 > set silhouettes true vol ignore padd value None m stats None -0.2371344417333603 0.35903599858283997 vol ignore padd value None m stats None -0.16461524367332458 0.2752765417098999 vol ignore padd value None m stats None -0.1281111091375351 0.26489919424057007 vol ignore padd value None m stats None -0.1759013831615448 0.32811522483825684 > volume #3 #5 #6 transparency 0.5 > surface dust #1-8 size 5 > color zone #4 near #2 #1 distance 6 > view matrix camera 0.90725,-0.19704,-0.37157,-16.501,-0.32977,0.21509,-0.91923,-349.08,0.26104,0.95651,0.13017,329.98 > save /Users/lijuanyin/project/kre33_90S/figures/for_ed/kre33_position1.png supersample 3 > view matrix camera 0.13183,-0.19704,-0.97149,-399.77,-0.96096,0.21509,-0.17403,141.95,0.24324,0.95651,-0.16098,142.35 > save /Users/lijuanyin/project/kre33_90S/figures/for_ed/kre33_position2.png supersample 3 > lighting full > lighting soft > lighting full > view matrix camera 0.90725,-0.19704,-0.37157,-16.501,-0.32977,0.21509,-0.91923,-349.08,0.26104,0.95651,0.13017,329.98 > save /Users/lijuanyin/project/kre33_90S/figures/for_ed/kre33_position1.png supersample 3 > color #2/R dark green > color zone #4 near #2 #1 distance 6 > view matrix camera 0.90725,-0.19704,-0.37157,-16.501,-0.32977,0.21509,-0.91923,-349.08,0.26104,0.95651,0.13017,329.98 > save /Users/lijuanyin/project/kre33_90S/figures/for_ed/kre33_position1.png supersample 3 > lighting soft > save /Users/lijuanyin/project/kre33_90S/figures/for_ed/kre33_position1.png supersample 3 > lighting full > view matrix camera 0.13183,-0.19704,-0.97149,-399.77,-0.96096,0.21509,-0.17403,141.95,0.24324,0.95651,-0.16098,142.35 > save /Users/lijuanyin/project/kre33_90S/figures/for_ed/kre33_position2.png supersample 3 > volume #4 hide > hide #1 #2 target r > volume #5 #6 show > color #5 #6 light gray > color #7/X forest green > color #7/B hot pink > color #7/S coral > color #7/N blue violet > color #7/O turquoise > color #9 orange > color #8 yellow > color #10 khaki > color zone #5 near #7 distance 6 > color zone #6 near #7 #8 #9 #10 distance 20 > view matrix camera 0.90725,-0.19704,-0.37157,-16.501,-0.32977,0.21509,-0.91923,-349.08,0.26104,0.95651,0.13017,329.98 > lighting full > save /Users/lijuanyin/project/kre33_90S/figures/for_ed/nop14_position1.png supersample 3 > view matrix camera 0.13183,-0.19704,-0.97149,-399.77,-0.96096,0.21509,-0.17403,141.95,0.24324,0.95651,-0.16098,142.35 > save /Users/lijuanyin/project/kre33_90S/figures/for_ed/nop14_position2.png supersample 3 > close > open /Users/lijuanyin/project/kre33_90S/figures/figure2/chainM.pdb Chain information for chainM.pdb #1 --- Chain | Description M | No description available > close > open /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_utp.pdb Summary of feedback from opening /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_utp.pdb --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 3723 messages similar to the above omitted Chain information for c5_utp.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E I | No description available F | No description available G | No description available H | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available X | No description available Y | No description available Z | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_ribo.pdb Chain information for c5_ribo.pdb #2 --- Chain | Description 1 | No description available 2 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N d | No description available O | No description available P | No description available Q | No description available R S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available e g | No description available f | No description available h | No description available i | No description available j m | No description available k | No description available l | No description available n | No description available o | No description available p | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure2/beak2.pdb Chain information for beak2.pdb #3 --- Chain | Description 2 | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure2/rrp12.pdb Chain information for rrp12.pdb #4 --- Chain | Description s | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure2/chainM.pdb Chain information for chainM.pdb #5 --- Chain | Description M | No description available > color #1 #2 light gray > show #1 #2 target r > hide #1 #2 #4 #5 target a > show #2/1 /2 #3 target a > nucleotides #2/1 ladder > nucleotides #2/2 ladder > nucleotides #3 ladder > ribbon style protein modeh tube rad 2 sides 24 > ribbon style nucleic xsect oval width 1.6 thick 1.6 > cartoon style protein xsection oval width 1 thickness 1 > cartoon style strand xsection rectangle width 2 thickness 0.5 > ui mousemode rightMode zoom > color #1 #2 light gray > color #2/R dark green > color #2/S lime > color #2/W cornflower blue > color #2/Y hot pink > color #2/Z red > color #2/X forest green > color #1/B hot pink > color #1/S coral > color #2/N blue violet > color #2/O turquoise > color #4 orange > color #3 yellow > color #5 khaki > view matrix camera 0.90725,-0.19704,-0.37157,-16.501,-0.32977,0.21509,-0.91923,-349.08,0.26104,0.95651,0.13017,329.98 > save /Users/lijuanyin/project/kre33_90S/figures/for_ed/model_b2_v1 supersample 3 Missing filename suffix /Users/lijuanyin/project/kre33_90S/figures/for_ed/model_b2_v1 > turn y 60 > view matrix camera 0.13183,-0.19704,-0.97149,-399.77,-0.96096,0.21509,-0.17403,141.95,0.24324,0.95651,-0.16098,142.35 > save /Users/lijuanyin/project/kre33_90S/figures/for_ed/model_b2_v2.png supersample 3 > view matrix camera 0.90725,-0.19704,-0.37157,-16.501,-0.32977,0.21509,-0.91923,-349.08,0.26104,0.95651,0.13017,329.98 > save /Users/lijuanyin/project/kre33_90S/figures/for_ed/model_b2_v1.png supersample 3 > turn y 60 > view matrix camera 0.13183,-0.19704,-0.97149,-399.77,-0.96096,0.21509,-0.17403,141.95,0.24324,0.95651,-0.16098,142.35 > save /Users/lijuanyin/project/kre33_90S/figures/for_ed/model_b2_v2.png supersample 3 > view matrix camera 0.90725,-0.19704,-0.37157,-16.501,-0.32977,0.21509,-0.91923,-349.08,0.26104,0.95651,0.13017,329.98 > set silhouettes false > lighting soft > lighting full > set silhouettes true > close > open /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_utp.pdb Summary of feedback from opening /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_utp.pdb --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 3723 messages similar to the above omitted Chain information for c5_utp.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E I | No description available F | No description available G | No description available H | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available X | No description available Y | No description available Z | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_ribo.pdb Chain information for c5_ribo.pdb #2 --- Chain | Description 1 | No description available 2 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N d | No description available O | No description available P | No description available Q | No description available R S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available e g | No description available f | No description available h | No description available i | No description available j m | No description available k | No description available l | No description available n | No description available o | No description available p | No description available > open /Users/lijuanyin/project/kre33_90S/job028_class3d_job026_8c/c5_and_c146ofc2/second_refine/post_2/postprocess_masked.mrc Summary of feedback from opening /Users/lijuanyin/project/kre33_90S/job028_class3d_job026_8c/c5_and_c146ofc2/second_refine/post_2/postprocess_masked.mrc --- notes | vol ignore padd value None m stats None -0.22822514176368713 0.3320360779762268 Opened postprocess_masked.mrc, grid size 480,480,480, pixel 1.08, shown at level 0.0347, step 2, values float32 > open /Users/lijuanyin/project/kre33_90S/figures/for_ed/kre33_map.mrc Summary of feedback from opening /Users/lijuanyin/project/kre33_90S/figures/for_ed/kre33_map.mrc --- notes | vol ignore padd value None m stats None -0.14686203002929688 0.253886878490448 Opened kre33_map.mrc, grid size 480,480,480, pixel 1.08, shown at level -2.76e-05, step 2, values float32 > open /Users/lijuanyin/project/kre33_90S/figures/figure2/emg1_map.mrc Summary of feedback from opening /Users/lijuanyin/project/kre33_90S/figures/figure2/emg1_map.mrc --- notes | vol ignore padd value None m stats None -0.11638116836547852 0.22486688196659088 Opened emg1_map.mrc, grid size 480,480,480, pixel 1.08, shown at level -1.56e-05, step 2, values float32 > open /Users/lijuanyin/project/kre33_90S/figures/figure2/rrp12_map_from_job189.mrc Summary of feedback from opening /Users/lijuanyin/project/kre33_90S/figures/figure2/rrp12_map_from_job189.mrc --- notes | vol ignore padd value None m stats None -0.17061135172843933 0.3109600841999054 Opened rrp12_map_from_job189.mrc, grid size 480,480,480, pixel 1.08, shown at level -3.87e-05, step 2, values float32 > open /Users/lijuanyin/project/kre33_90S/figures/figure2/emg1_complex.pdb Chain information for emg1_complex.pdb #7 --- Chain | Description B | No description available N | No description available O | No description available S | No description available X | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure2/beak2.pdb Chain information for beak2.pdb #8 --- Chain | Description 2 | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure2/rrp12.pdb Chain information for rrp12.pdb #9 --- Chain | Description s | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure2/chainM.pdb Chain information for chainM.pdb #10 --- Chain | Description M | No description available > color #3 #5 #6 light gray > volume #3 #5 #6 transparency 0.5 > volume #3 step 1 level 0.04 > volume #4 step 1 level 0.01 > volume #5 step 1 level 0.04 > volume #6 step 1 level 0.04 > surface dust #1-8 size 5 > set bgColor white > lighting full > color #1 #2 light gray > color #2/R dark green > color #2/S lime > color #2/W cornflower blue > color #2/Y hot pink > color #2/Z red > hide #1 #2 #7 #8 #9 target a > hide #7 #8 #9 #10 target r > show #2/R /S /W /Z /Y target r > windowsize 600 800 > set silhouettes true > color zone #4 near #2 #1 distance 6 vol ignore padd value None m stats None -0.2371344417333603 0.35903599858283997 vol ignore padd value None m stats None -0.16461524367332458 0.2752765417098999 vol ignore padd value None m stats None -0.1281111091375351 0.26489919424057007 vol ignore padd value None m stats None -0.1759013831615448 0.32811522483825684 > surface dust #1-8 size 5 > view matrix camera 0.90725,-0.19704,-0.37157,-16.501,-0.32977,0.21509,-0.91923,-349.08,0.26104,0.95651,0.13017,329.98 > lighting full > view matrix camera 0.13183,-0.19704,-0.97149,-399.77,-0.96096,0.21509,-0.17403,141.95,0.24324,0.95651,-0.16098,142.35 could not retrieve bundle list from toolshed Unknown command: screencapture 43,87, 643,887 /Users/lijuanyin/project/kre33_90S/figures/for_ed/kre33_position3.png > volume #4 hide > hide #1 #2 target r > volume #5 #6 show > color #5 #6 light gray > color #7/X forest green > color #7/B hot pink > color #7/S coral > color #7/N blue violet > color #7/O turquoise > color #9 orange > color #8 yellow > color #10 khaki > color zone #5 near #7 distance 6 > color zone #6 near #7 #8 #9 #10 distance 20 > view matrix camera 0.90725,-0.19704,-0.37157,-16.501,-0.32977,0.21509,-0.91923,-349.08,0.26104,0.95651,0.13017,329.98 > view matrix camera 0.13183,-0.19704,-0.97149,-399.77,-0.96096,0.21509,-0.17403,141.95,0.24324,0.95651,-0.16098,142.35 Unknown command: screencapture 43,87, 643,887 /Users/lijuanyin/project/kre33_90S/figures/for_ed/nop14_position2.png > close > open /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_utp.pdb Summary of feedback from opening /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_utp.pdb --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 3723 messages similar to the above omitted Chain information for c5_utp.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E I | No description available F | No description available G | No description available H | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available X | No description available Y | No description available Z | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_ribo.pdb Chain information for c5_ribo.pdb #2 --- Chain | Description 1 | No description available 2 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N d | No description available O | No description available P | No description available Q | No description available R S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available e g | No description available f | No description available h | No description available i | No description available j m | No description available k | No description available l | No description available n | No description available o | No description available p | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure2/beak2.pdb Chain information for beak2.pdb #3 --- Chain | Description 2 | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure2/rrp12.pdb Chain information for rrp12.pdb #4 --- Chain | Description s | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure2/chainM.pdb Chain information for chainM.pdb #5 --- Chain | Description M | No description available > color #1 #2 light gray > show #1 #2 target r > hide #1 #2 #4 #5 target a > show #2/1 /2 #3 target a > nucleotides #2/1 ladder > nucleotides #2/2 ladder > nucleotides #3 ladder > ribbon style protein modeh tube rad 2 sides 24 > ribbon style nucleic xsect oval width 1.6 thick 1.6 > cartoon style protein xsection oval width 1 thickness 1 > cartoon style strand xsection rectangle width 2 thickness 0.5 > color #1 #2 light gray > color #2/R dark green > color #2/S lime > color #2/W cornflower blue > color #2/Y hot pink > color #2/Z red > color #2/X forest green > color #1/B hot pink > color #1/S coral > color #2/N blue violet > color #2/O turquoise > color #4 orange > color #3 yellow > color #5 khaki > hide #1 #2 target r > hide #2 target a > show #2/X /N /O #1/B /S target r > windowsize 800 650 > view matrix camera position: 0.16493,-0.88576,-0.43386,-42.03,-0.76226,-0.39362,0.51383,445.59,-0.62591,0.24597,-0.7401,-91.53 model positions: #1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0 > show #2/R /S /W /Z /Y target r > hide #2/X /N /O #1/B /S #3 #4 #5 target r > hide #3 #4 #5 target a > view matrix camera position: 0.38879,0.83958,-0.3794,83.118,-0.83747,0.15039,-0.52539,105.46,-0.38405,0.522,0.76159,588.52 model positions: #1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0 Unknown command: screencapture -i 43,87, 843,737 /Users/lijuanyin/project/kre33_90S/figures/for_ed/kre33_complex.png > windowsize 800 650 > show selAtoms > windowsize 850 700 > windowsize 850 720 > windowsize 850 750 > windowsize 850 745 > close > open /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_utp.pdb Summary of feedback from opening /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_utp.pdb --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 3723 messages similar to the above omitted Chain information for c5_utp.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E I | No description available F | No description available G | No description available H | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available X | No description available Y | No description available Z | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_ribo.pdb Chain information for c5_ribo.pdb #2 --- Chain | Description 1 | No description available 2 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N d | No description available O | No description available P | No description available Q | No description available R S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available e g | No description available f | No description available h | No description available i | No description available j m | No description available k | No description available l | No description available n | No description available o | No description available p | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure2/beak2.pdb Chain information for beak2.pdb #3 --- Chain | Description 2 | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure2/rrp12.pdb Chain information for rrp12.pdb #4 --- Chain | Description s | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure2/chainM.pdb Chain information for chainM.pdb #5 --- Chain | Description M | No description available > color #1 #2 light gray > show #1 #2 target r > hide #1 #2 #4 #5 target a > show #2/1 /2 #3 target a > nucleotides #2/1 ladder > nucleotides #2/2 ladder > nucleotides #3 ladder > ribbon style protein modeh tube rad 2 sides 24 > ribbon style nucleic xsect oval width 1.6 thick 1.6 > cartoon style protein xsection oval width 1 thickness 1 > cartoon style strand xsection rectangle width 2 thickness 0.5 > color #1 #2 light gray > color #2/R dark green > color #2/S lime > color #2/W cornflower blue > color #2/Y hot pink > color #2/Z red > color #2/X forest green > color #1/B hot pink > color #1/S coral > color #2/N blue violet > color #2/O turquoise > color #4 orange > color #3 yellow > color #5 khaki > close > open /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_utp.pdb Summary of feedback from opening /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_utp.pdb --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 3723 messages similar to the above omitted Chain information for c5_utp.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E I | No description available F | No description available G | No description available H | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available X | No description available Y | No description available Z | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_ribo.pdb Chain information for c5_ribo.pdb #2 --- Chain | Description 1 | No description available 2 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N d | No description available O | No description available P | No description available Q | No description available R S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available e g | No description available f | No description available h | No description available i | No description available j m | No description available k | No description available l | No description available n | No description available o | No description available p | No description available > open /Users/lijuanyin/project/kre33_90S/job028_class3d_job026_8c/c5_and_c146ofc2/second_refine/post_2/postprocess_masked.mrc Summary of feedback from opening /Users/lijuanyin/project/kre33_90S/job028_class3d_job026_8c/c5_and_c146ofc2/second_refine/post_2/postprocess_masked.mrc --- notes | vol ignore padd value None m stats None -0.22822514176368713 0.3320360779762268 Opened postprocess_masked.mrc, grid size 480,480,480, pixel 1.08, shown at level 0.0347, step 2, values float32 > open /Users/lijuanyin/project/kre33_90S/figures/for_ed/kre33_map.mrc Summary of feedback from opening /Users/lijuanyin/project/kre33_90S/figures/for_ed/kre33_map.mrc --- notes | vol ignore padd value None m stats None -0.14686203002929688 0.253886878490448 Opened kre33_map.mrc, grid size 480,480,480, pixel 1.08, shown at level -2.76e-05, step 2, values float32 > open /Users/lijuanyin/project/kre33_90S/figures/figure2/emg1_map.mrc Summary of feedback from opening /Users/lijuanyin/project/kre33_90S/figures/figure2/emg1_map.mrc --- notes | vol ignore padd value None m stats None -0.11638116836547852 0.22486688196659088 Opened emg1_map.mrc, grid size 480,480,480, pixel 1.08, shown at level -1.56e-05, step 2, values float32 > open /Users/lijuanyin/project/kre33_90S/figures/figure2/rrp12_map_from_job189.mrc Summary of feedback from opening /Users/lijuanyin/project/kre33_90S/figures/figure2/rrp12_map_from_job189.mrc --- notes | vol ignore padd value None m stats None -0.17061135172843933 0.3109600841999054 Opened rrp12_map_from_job189.mrc, grid size 480,480,480, pixel 1.08, shown at level -3.87e-05, step 2, values float32 > open /Users/lijuanyin/project/kre33_90S/figures/figure2/emg1_complex.pdb Chain information for emg1_complex.pdb #7 --- Chain | Description B | No description available N | No description available O | No description available S | No description available X | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure2/beak2.pdb Chain information for beak2.pdb #8 --- Chain | Description 2 | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure2/rrp12.pdb Chain information for rrp12.pdb #9 --- Chain | Description s | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure2/chainM.pdb Chain information for chainM.pdb #10 --- Chain | Description M | No description available > color #3 #5 #6 light gray > volume #3 #5 #6 transparency 0.5 > volume #3 step 1 level 0.04 > volume #4 step 1 level 0.01 > volume #5 step 1 level 0.04 > volume #6 step 1 level 0.04 > surface dust #1-8 size 5 > set bgColor white > lighting full > color #1 #2 light gray > color #2/R dark green > color #2/S lime > color #2/W cornflower blue > color #2/Y hot pink > color #2/Z red > hide #1 #2 #7 #8 #9 target a > hide #7 #8 #9 #10 target r > show #2/R /S /W /Z /Y target r vol ignore padd value None m stats None -0.2371344417333603 0.35903599858283997 vol ignore padd value None m stats None -0.16461524367332458 0.2752765417098999 vol ignore padd value None m stats None -0.1281111091375351 0.26489919424057007 vol ignore padd value None m stats None -0.1759013831615448 0.32811522483825684 > color zone #4 near #2 #1 distance 6 > windowsize 600 800 > set silhouettes true > surface dust #1-8 size 5 > view matrix camera 0.90725,-0.19704,-0.37157,-16.501,-0.32977,0.21509,-0.91923,-349.08,0.26104,0.95651,0.13017,329.98 > windowsize 650 850 Unknown command: screencapture -R 43,87,643,887 /Users/lijuanyin/project/kre33_90S/figures/for_ed/kre33_position1.png > windowsize 643 887 > windowsize 643 867 > windowsize 643 887 Unknown command: screencapture -R 43,87,643,887 /Users/lijuanyin/project/kre33_90S/figures/for_ed/kre33_position1.png > view matrix camera 0.13183,-0.19704,-0.97149,-399.77,-0.96096,0.21509,-0.17403,141.95,0.24324,0.95651,-0.16098,142.35 > volume #4 hide > hide #1 #2 target r > volume #5 #6 show > color #5 #6 light gray > color #7/X forest green > color #7/B hot pink > color #7/S coral > color #7/N blue violet > color #7/O turquoise > color #9 orange > color #8 yellow > color #10 khaki > color zone #5 near #7 distance 6 > color zone #6 near #7 #8 #9 #10 distance 20 > view matrix camera 0.90725,-0.19704,-0.37157,-16.501,-0.32977,0.21509,-0.91923,-349.08,0.26104,0.95651,0.13017,329.98 Unknown command: screencapture -R 43,87,643,887 /Users/lijuanyin/project/kre33_90S/figures/for_ed/nop14_position1.png -P > view matrix camera 0.13183,-0.19704,-0.97149,-399.77,-0.96096,0.21509,-0.17403,141.95,0.24324,0.95651,-0.16098,142.35 Unknown command: screencapture -R 43,87,643,887 /Users/lijuanyin/project/kre33_90S/figures/for_ed/nop14_position2.png > close > open /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_utp.pdb Summary of feedback from opening /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_utp.pdb --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 3723 messages similar to the above omitted Chain information for c5_utp.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E I | No description available F | No description available G | No description available H | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available X | No description available Y | No description available Z | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_ribo.pdb Chain information for c5_ribo.pdb #2 --- Chain | Description 1 | No description available 2 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N d | No description available O | No description available P | No description available Q | No description available R S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available e g | No description available f | No description available h | No description available i | No description available j m | No description available k | No description available l | No description available n | No description available o | No description available p | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure2/beak2.pdb Chain information for beak2.pdb #3 --- Chain | Description 2 | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure2/rrp12.pdb Chain information for rrp12.pdb #4 --- Chain | Description s | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure2/chainM.pdb Chain information for chainM.pdb #5 --- Chain | Description M | No description available > color #1 #2 light gray > show #1 #2 target r > hide #1 #2 #4 #5 target a > show #2/1 /2 #3 target a > nucleotides #2/1 ladder > nucleotides #2/2 ladder > nucleotides #3 ladder > ribbon style protein modeh tube rad 2 sides 24 > ribbon style nucleic xsect oval width 1.6 thick 1.6 > cartoon style protein xsection oval width 1 thickness 1 > cartoon style strand xsection rectangle width 2 thickness 0.5 > color #1 #2 light gray > color #2/R dark green > color #2/S lime > color #2/W cornflower blue > color #2/Y hot pink > color #2/Z red > color #2/X forest green > color #1/B hot pink > color #1/S coral > color #2/N blue violet > color #2/O turquoise > color #4 orange > color #3 yellow > color #5 khaki > view matrix camera -0.24562,-0.17531,-0.95338,-349.57,-0.88509,0.44166,0.14681,364.18,0.39533,0.87989,-0.26364,90.863 > view matrix camera 0.90725,-0.19704,-0.37157,-16.501,-0.32977,0.21509,-0.91923,-349.08,0.26104,0.95651,0.13017,329.98 Unknown command: screencapture -R 43,87,643,887 /Users/lijuanyin/project/kre33_90S/figures/for_ed/model_b2_v1.png > view matrix camera 0.13183,-0.19704,-0.97149,-399.77,-0.96096,0.21509,-0.17403,141.95,0.24324,0.95651,-0.16098,142.35 > hide #1 #2 target r > hide #2 target a > show #2/X /N /O #1/B /S target r > windowsize 843 737 Traceback (most recent call last): File "/Applications/ChimeraX 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/ui/graphics.py", line 80, in resizeEvent v.draw(check_for_changes = False) File "/Applications/ChimeraX 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/view.py", line 159, in draw self._draw_scene(camera, drawings) File "/Applications/ChimeraX 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/view.py", line 213, in _draw_scene draw_depth(r, opaque_drawings) File "/Applications/ChimeraX 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/drawing.py", line 1379, in draw_depth draw_opaque(r, drawings) File "/Applications/ChimeraX 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/drawing.py", line 1360, in draw_opaque _draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS) File "/Applications/ChimeraX 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/drawing.py", line 1371, in _draw_multiple d.draw(renderer, draw_pass) File "/Applications/ChimeraX 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/drawing.py", line 684, in draw if not self.display: File "/Applications/ChimeraX 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/drawing.py", line 311, in get_display return self._any_displayed_positions and len(self._positions) > 0 TypeError: object of type 'NoneType' has no len() TypeError: object of type 'NoneType' has no len() File "/Applications/ChimeraX 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/drawing.py", line 311, in get_display return self._any_displayed_positions and len(self._positions) > 0 See log for complete Python traceback. OpenGL version: 4.1 ATI-2.4.9 OpenGL renderer: AMD Radeon Pro 455 OpenGL Engine OpenGL vendor: ATI Technologies Inc.
Change History (2)
comment:1 by , 7 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → self._positions is None |
| Version: | → 0.9 |
comment:2 by , 7 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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