![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 12 months ago
Closed 12 months ago
#16205 closed defect (can't reproduce)
cartoon style nucleic: glDrawBuffer: invalid operation
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | Greg Couch | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.14.0-427.20.1.el9_4.x86_64-x86_64-with-glibc2.34
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /yonath_group/disha/Thesis_figures/rps26_TISU_control_1207_zoom.cxs
Opened multibody_60s_40s_rps26_control_tisu_tRNA_aligned2shiny.mrc as #1, grid
size 480,480,480, pixel 0.842, shown at level 0.004, step 1, values float32
Opened multibody_60s_40s_rps26_control_tisu_tRNA_aligned2shiny.mrc as #3, grid
size 480,480,480, pixel 0.842, shown at step 1, values float32
Log from Thu Aug 29 17:07:16 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /yonath_group/disha/Thesis_figures/rps26_TISU_control_zoom_mRNA.cxs
Opened multibody_60s_40s_rps26_control_tisu_tRNA_aligned2shiny.mrc as #1, grid
size 480,480,480, pixel 0.842, shown at level 0.004, step 1, values float32
Opened multibody_60s_40s_rps26_control_tisu_tRNA_aligned2shiny.mrc as #3, grid
size 480,480,480, pixel 0.842, shown at level 0.004, step 1, values float32
Log from Wed Aug 28 17:08:09 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /yonath_group/disha/Thesis_figures/rps26_kozak_control_whole_ribo.cxs
> format session
Opened
60s_40s_multibody_aligned2shiny_kozak_control_tRNA_with_blush_inverted_again.mrc
as #1, grid size 480,480,480, pixel 0.842, shown at level 0.005, step 1,
values float32
Opened
60s_40s_multibody_aligned2shiny_kozak_control_tRNA_with_blush_inverted_again.mrc
as #3, grid size 480,480,480, pixel 0.842, shown at level 0.005, step 1,
values float32
Log from Wed Aug 28 16:36:21 2024 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /archive/processing/disha/20240106_disha_RPS19_L64P_80S_mutant/relion/Refine3D/3d_ref_unsharp2/run_class001.mrc
Opened run_class001.mrc as #1, grid size 480,480,480, pixel 0.826, shown at
level 0.00731, step 2, values float32
> volume #1 level 0.00261
> close session
> open
> /archive/processing/disha/20240617_disha_mouse_female_wildtype_80s/relion/Class3D/3d_class/run_it025_class001.mrc
> /archive/processing/disha/20240617_disha_mouse_female_wildtype_80s/relion/Class3D/3d_class/run_it025_class002.mrc
> /archive/processing/disha/20240617_disha_mouse_female_wildtype_80s/relion/Class3D/3d_class/run_it025_class003.mrc
> /archive/processing/disha/20240617_disha_mouse_female_wildtype_80s/relion/Class3D/3d_class/run_it025_class004.mrc
> /archive/processing/disha/20240617_disha_mouse_female_wildtype_80s/relion/Class3D/3d_class/run_it025_class005.mrc
> /archive/processing/disha/20240617_disha_mouse_female_wildtype_80s/relion/Class3D/3d_class/run_it025_class006.mrc
> /archive/processing/disha/20240617_disha_mouse_female_wildtype_80s/relion/Class3D/3d_class/run_it025_class007.mrc
> /archive/processing/disha/20240617_disha_mouse_female_wildtype_80s/relion/Class3D/3d_class/run_it025_class008.mrc
> format mrc
Opened run_it025_class001.mrc as #1.1, grid size 480,480,480, pixel 0.824,
shown at level 0.00458, step 2, values float32
Opened run_it025_class002.mrc as #1.2, grid size 480,480,480, pixel 0.824,
shown at level 0.00425, step 2, values float32
Opened run_it025_class003.mrc as #1.3, grid size 480,480,480, pixel 0.824,
shown at level 0.00431, step 2, values float32
Opened run_it025_class004.mrc as #1.4, grid size 480,480,480, pixel 0.824,
shown at level 0.0048, step 2, values float32
Opened run_it025_class005.mrc as #1.5, grid size 480,480,480, pixel 0.824,
shown at level 0.00605, step 2, values float32
Opened run_it025_class006.mrc as #1.6, grid size 480,480,480, pixel 0.824,
shown at level 0.00458, step 2, values float32
Opened run_it025_class007.mrc as #1.7, grid size 480,480,480, pixel 0.824,
shown at level 0.00359, step 2, values float32
Opened run_it025_class008.mrc as #1.8, grid size 480,480,480, pixel 0.824,
shown at level 0.00609, step 2, values float32
> vop all level 0.009
> vop all level 0.002
> tile
8 models tiled
> close session
> open
> /archive/processing/disha/20240617_disha_mouse_female_wildtype_80s/relion/InitialModel/3d_ini_model_5/initial_model.mrc
Opened initial_model.mrc as #1, grid size 480,480,480, pixel 0.824, shown at
level 0.0382, step 2, values float32
> volume #1 level 0.008093
> close session
> open
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/Male_wildtype/class3_blush/maps/rps9_mwt_FR_combined_aligned2shiny_with_antiibiotic_p842_class3_with_blush.mrc
Opened
rps9_mwt_FR_combined_aligned2shiny_with_antiibiotic_p842_class3_with_blush.mrc
as #1, grid size 480,480,480, pixel 0.842, shown at level 0.0295, step 2,
values float32
> vop all level 0.002
> vop all level 0.009
> surface dust #1 size 8.42
> close session
> open
> /archive/processing/disha/RPS9_male_control_p3/relion/Refine3D/3d_ref_shiny_class2_with_blush/run_class001.mrc
Opened run_class001.mrc as #1, grid size 480,480,480, pixel 0.85, shown at
level 0.0203, step 2, values float32
> open
> /archive/processing/disha/RPS9_male_control_p3/relion/MultiBody/Multibody_class2/run_body001.mrc
> /archive/processing/disha/RPS9_male_control_p3/relion/MultiBody/Multibody_class2/run_body002.mrc
> /archive/processing/disha/RPS9_male_control_p3/relion/MultiBody/Multibody_class2/run_body003.mrc
Opened run_body001.mrc as #2.1, grid size 480,480,480, pixel 0.85, shown at
level 0.018, step 2, values float32
Opened run_body002.mrc as #2.2, grid size 480,480,480, pixel 0.85, shown at
level 0.00937, step 2, values float32
Opened run_body003.mrc as #2.3, grid size 480,480,480, pixel 0.85, shown at
level 0.00565, step 2, values float32
> vop all level 0.009
> ui tool show "Map Coordinates"
> ui tool show "Fit in Map"
> fitmap #2.1 inMap #1
Fit map run_body001.mrc in map run_class001.mrc using 460717 points
correlation = 0.9871, correlation about mean = 0.9279, overlap = 148
steps = 80, shift = 0.35, angle = 3.1 degrees
Position of run_body001.mrc (#2.1) relative to run_class001.mrc (#1)
coordinates:
Matrix rotation and translation
0.99905469 -0.03767077 -0.02169443 11.55869628
0.03695539 0.99878885 -0.03248277 -1.06110097
0.02289181 0.03165033 0.99923682 -10.53246662
Axis 0.59367101 -0.41272853 0.69080380
Axis point 38.45528148 305.48912718 0.00000000
Rotation angle (degrees) 3.09628142
Shift along axis 0.02414159
> fitmap #2.2 inMap #1
Fit map run_body002.mrc in map run_class001.mrc using 148467 points
correlation = 0.9842, correlation about mean = 0.8364, overlap = 33.93
steps = 72, shift = 0.774, angle = 2.61 degrees
Position of run_body002.mrc (#2.2) relative to run_class001.mrc (#1)
coordinates:
Matrix rotation and translation
0.99948876 0.02207305 0.02312999 -8.69916552
-0.02280903 0.99922585 0.03205399 0.16468963
-0.02240455 -0.03256517 0.99921847 13.00905448
Axis -0.71085515 0.50091115 -0.49373371
Axis point 0.00000000 397.05413628 2.00334992
Rotation angle (degrees) 2.60508855
Shift along axis -0.15666717
> fitmap #2.3 inMap #1
Fit map run_body003.mrc in map run_class001.mrc using 60995 points
correlation = 0.9642, correlation about mean = 0.677, overlap = 14.42
steps = 72, shift = 0.174, angle = 2.02 degrees
Position of run_body003.mrc (#2.3) relative to run_class001.mrc (#1)
coordinates:
Matrix rotation and translation
0.99993470 -0.01137432 0.00110915 3.12181099
0.01140498 0.99937933 -0.03332988 2.24795544
-0.00072935 0.03334036 0.99944379 -9.75095477
Axis 0.94596771 0.02608601 0.32320987
Axis point 0.00000000 292.14768869 62.11470115
Rotation angle (degrees) 2.01947409
Shift along axis -0.13983224
> vop resample #2 onGrid #1
Opened run_body001.mrc resampled as #3, grid size 480,480,480, pixel 0.85,
shown at step 1, values float32
Opened run_body002.mrc resampled as #4, grid size 480,480,480, pixel 0.85,
shown at step 1, values float32
Opened run_body003.mrc resampled as #5, grid size 480,480,480, pixel 0.85,
shown at step 1, values float32
> vop resample #2 onGrid #1
Opened run_body001.mrc resampled as #6, grid size 480,480,480, pixel 0.85,
shown at step 1, values float32
Opened run_body002.mrc resampled as #7, grid size 480,480,480, pixel 0.85,
shown at step 1, values float32
Opened run_body003.mrc resampled as #8, grid size 480,480,480, pixel 0.85,
shown at step 1, values float32
> close #6
> close #7
> close #8
> vop add #3-5 onGrid #1
Opened volume sum as #6, grid size 480,480,480, pixel 0.85, shown at step 1,
values float32
> save
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/Male_wildtype/class2_blush/maps/rps9_mwt_multibody_combined_aligned2shiny_with_antiibiotic_p842_class2_with_blush.mrc
> models #6
> save
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/Male_wildtype/class2_blush/maps/rps9_mwt_shiny_with_antiibiotic_p842_class2_with_blush.mrc
> models #1
> open
> /archive/processing/disha/RPS9_male_control_p3/relion/PostProcess/FR_40S_body_class2/postprocess_masked.mrc
Opened postprocess_masked.mrc as #7, grid size 480,480,480, pixel 0.842, shown
at level 0.00997, step 2, values float32
> open
> /archive/processing/disha/RPS9_male_control_p3/relion/PostProcess/FR_40S_head_class2/postprocess_masked.mrc
Opened postprocess_masked.mrc as #8, grid size 480,480,480, pixel 0.842, shown
at level 0.000738, step 2, values float32
> open
> /archive/processing/disha/RPS9_male_control_p3/relion/PostProcess/FR_60S_class2/postprocess_masked.mrc
Opened postprocess_masked.mrc as #9, grid size 480,480,480, pixel 0.842, shown
at level 0.0288, step 2, values float32
> fitmap #7 inMap #1
Fit map postprocess_masked.mrc in map run_class001.mrc using 138139 points
correlation = 0.937, correlation about mean = 0.6602, overlap = 40.3
steps = 108, shift = 3.89, angle = 2.47 degrees
Position of postprocess_masked.mrc (#7) relative to run_class001.mrc (#1)
coordinates:
Matrix rotation and translation
0.99958139 0.01981063 0.02108506 -6.11020558
-0.02047257 0.99928915 0.03165536 2.27633203
-0.02044296 -0.03207377 0.99927642 13.53443622
Axis -0.74040027 0.48246939 -0.46800720
Axis point 0.00000000 413.24745438 -73.48117368
Rotation angle (degrees) 2.46659730
Shift along axis -0.71195521
> fitmap #8 inMap #1
Fit map postprocess_masked.mrc in map run_class001.mrc using 137995 points
correlation = 0.8366, correlation about mean = 0.646, overlap = 22.46
steps = 88, shift = 4.04, angle = 1.82 degrees
Position of postprocess_masked.mrc (#8) relative to run_class001.mrc (#1)
coordinates:
Matrix rotation and translation
0.99994675 -0.01031302 0.00038139 5.21293975
0.01031982 0.99949706 -0.02998534 4.80935006
-0.00007196 0.02998768 0.99955027 -7.45308205
Axis 0.94557948 0.00714778 0.32531271
Axis point 0.00000000 278.40854859 155.11514167
Rotation angle (degrees) 1.81728605
Shift along axis 2.53904272
> fitmap #9 inMap #1
Fit map postprocess_masked.mrc in map run_class001.mrc using 138037 points
correlation = 0.9524, correlation about mean = 0.6233, overlap = 152.8
steps = 80, shift = 3.15, angle = 3.09 degrees
Position of postprocess_masked.mrc (#9) relative to run_class001.mrc (#1)
coordinates:
Matrix rotation and translation
0.99905482 -0.03763144 -0.02175627 13.38892350
0.03691767 0.99879528 -0.03232762 0.73292557
0.02294659 0.03149387 0.99924051 -8.58632381
Axis 0.59182584 -0.41453599 0.69130463
Axis point -27.99672011 330.00490042 0.00000000
Rotation angle (degrees) 3.09083856
Shift along axis 1.68432136
> vop all level 0.009
> fitmap #8 inMap #1
Fit map postprocess_masked.mrc in map run_class001.mrc using 66938 points
correlation = 0.9145, correlation about mean = 0.6511, overlap = 20.03
steps = 28, shift = 0.0257, angle = 0.0335 degrees
Position of postprocess_masked.mrc (#8) relative to run_class001.mrc (#1)
coordinates:
Matrix rotation and translation
0.99994581 -0.01040801 0.00020871 5.28737261
0.01040953 0.99947946 -0.03053611 4.88439493
0.00010922 0.03053663 0.99953364 -7.66167869
Axis 0.94652190 0.00154183 0.32263590
Axis point 0.00000000 280.10793407 155.05152718
Rotation angle (degrees) 1.84877785
Shift along axis 2.54021223
> vop add #7-9 onGrid #1
Opened volume sum as #10, grid size 480,480,480, pixel 0.85, shown at step 1,
values float32
> save
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/Male_wildtype/class2_blush/maps/rps9_mwt_FR_combined_aligned2shiny_with_antiibiotic_p842_class2_with_blush.mrc
> models #10
> close session
> open
> /archive/processing/disha/20230807_female_mt_rps9_antibiotic/relion/Refine3D/3d_ref_shiny_with_blush_class245/run_class001.mrc
Opened run_class001.mrc as #1, grid size 480,480,480, pixel 0.79, shown at
level 0.011, step 2, values float32
> open
> /archive/processing/disha/20230807_female_mt_rps9_antibiotic/relion/MultiBody/Multibody_class245_with_blush/run_body001.mrc
> /archive/processing/disha/20230807_female_mt_rps9_antibiotic/relion/MultiBody/Multibody_class245_with_blush/run_body002.mrc
> /archive/processing/disha/20230807_female_mt_rps9_antibiotic/relion/MultiBody/Multibody_class245_with_blush/run_body003.mrc
Opened run_body001.mrc as #2.1, grid size 480,480,480, pixel 0.79, shown at
level 0.00991, step 2, values float32
Opened run_body002.mrc as #2.2, grid size 480,480,480, pixel 0.79, shown at
level 0.00472, step 2, values float32
Opened run_body003.mrc as #2.3, grid size 480,480,480, pixel 0.79, shown at
level 0.00282, step 2, values float32
> vop all level 0.009
> vop all level 0.005
> ui tool show "Fit in Map"
> ui tool show "Map Coordinates"
> fitmap #2.1 inMap #1
Fit map run_body001.mrc in map run_class001.mrc using 450035 points
correlation = 0.9954, correlation about mean = 0.9745, overlap = 41.55
steps = 112, shift = 0.325, angle = 2.67 degrees
Position of run_body001.mrc (#2.1) relative to run_class001.mrc (#1)
coordinates:
Matrix rotation and translation
0.99894273 0.00648124 -0.04551291 9.09978284
-0.00612675 0.99994984 0.00792393 -0.88729775
0.04556198 -0.00763670 0.99893232 -6.98035836
Axis -0.16686840 -0.97666502 -0.13520495
Axis point 156.96443131 0.00000000 197.36243046
Rotation angle (degrees) 2.67241030
Shift along axis 0.29190547
> fitmap #2.2 inMap #1
Fit map run_body002.mrc in map run_class001.mrc using 127720 points
correlation = 0.9813, correlation about mean = 0.8764, overlap = 11.46
steps = 68, shift = 0.309, angle = 2.25 degrees
Position of run_body002.mrc (#2.2) relative to run_class001.mrc (#1)
coordinates:
Matrix rotation and translation
0.99923250 -0.00750397 0.03844620 -2.96590990
0.00757129 0.99997005 -0.00160561 -1.44704733
-0.03843300 0.00189547 0.99925938 7.44343237
Axis 0.04464440 0.98033315 0.19223370
Axis point 192.71571648 0.00000000 80.85213452
Rotation angle (degrees) 2.24718669
Shift along axis -0.12012118
> fitmap #2.3 inMap #1
Fit map run_body003.mrc in map run_class001.mrc using 58105 points
correlation = 0.9758, correlation about mean = 0.838, overlap = 4.815
steps = 60, shift = 0.102, angle = 2.36 degrees
Position of run_body003.mrc (#2.3) relative to run_class001.mrc (#1)
coordinates:
Matrix rotation and translation
0.99921743 0.03955041 -0.00053771 -4.51115974
-0.03955399 0.99914928 -0.01167011 7.78605287
0.00007569 0.01168225 0.99993176 -1.46887413
Axis 0.28312202 -0.00743687 -0.95905506
Axis point 194.31280333 118.43279527 0.00000000
Rotation angle (degrees) 2.36359442
Shift along axis 0.07361868
> vop resample #2 onGrid #1
Opened run_body001.mrc resampled as #3, grid size 480,480,480, pixel 0.824,
shown at step 1, values float32
Opened run_body002.mrc resampled as #4, grid size 480,480,480, pixel 0.824,
shown at step 1, values float32
Opened run_body003.mrc resampled as #5, grid size 480,480,480, pixel 0.824,
shown at step 1, values float32
> vop add #3-5 onGrid #1
Opened volume sum as #6, grid size 480,480,480, pixel 0.824, shown at step 1,
values float32
> save
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/female_mutant/class_245/new_maps/rps9_fmt_multibody_combined_aligned2shiny_with_antiibiotic_p824_class245_with_blush.mrc
> models #6
> open
> /archive/processing/disha/20230807_female_mt_rps9_antibiotic/relion/PostProcess/40S_body_FR_class245/postprocess_masked.mrc
Opened postprocess_masked.mrc as #7, grid size 480,480,480, pixel 0.824, shown
at level 0.00444, step 2, values float32
> open
> /archive/processing/disha/20230807_female_mt_rps9_antibiotic/relion/PostProcess/40S_head_FR_class_245/postprocess_masked.mrc
Opened postprocess_masked.mrc as #8, grid size 480,480,480, pixel 0.824, shown
at level 0.000619, step 2, values float32
> open
> /archive/processing/disha/20230807_female_mt_rps9_antibiotic/relion/PostProcess/60S_FR_class_245/postprocess_masked.mrc
Opened postprocess_masked.mrc as #9, grid size 480,480,480, pixel 0.824, shown
at level 0.00998, step 2, values float32
> vop all level 0.005
> fitmap #7 inMap #1
Fit map postprocess_masked.mrc in map run_class001.mrc using 124516 points
correlation = 0.9435, correlation about mean = 0.7496, overlap = 13.42
steps = 112, shift = 1.82, angle = 3.28 degrees
Position of postprocess_masked.mrc (#7) relative to run_class001.mrc (#1)
coordinates:
Matrix rotation and translation
0.99876609 -0.01272847 0.04800293 -2.88949369
0.01135226 0.99951976 0.02883371 -6.98238206
-0.04834688 -0.02825319 0.99843094 17.03562797
Axis -0.49835078 0.84110358 0.21021717
Axis point 353.53049191 0.00000000 78.12409221
Rotation angle (degrees) 3.28346021
Shift along axis -0.85174359
> fitmap #8 inMap #1
Fit map postprocess_masked.mrc in map run_class001.mrc using 55419 points
correlation = 0.9498, correlation about mean = 0.7421, overlap = 5.095
steps = 76, shift = 3.16, angle = 3.57 degrees
Position of postprocess_masked.mrc (#8) relative to run_class001.mrc (#1)
coordinates:
Matrix rotation and translation
0.99813540 0.06086350 -0.00462121 -7.09127620
-0.06080077 0.99806937 0.01268049 7.65710703
0.00538407 -0.01237588 0.99990892 3.51093470
Axis -0.20106232 -0.08028643 -0.97628276
Axis point 118.39317212 128.78225716 0.00000000
Rotation angle (degrees) 3.57241173
Shift along axis -2.61663832
> fitmap #9 inMap #1
Fit map postprocess_masked.mrc in map run_class001.mrc using 322671 points
correlation = 0.9524, correlation about mean = 0.8047, overlap = 40.76
steps = 104, shift = 2.22, angle = 4.44 degrees
Position of postprocess_masked.mrc (#9) relative to run_class001.mrc (#1)
coordinates:
Matrix rotation and translation
0.99736493 0.02649498 -0.06753682 9.27069004
-0.02466175 0.99930827 0.02783497 0.60773733
0.06822759 -0.02609605 0.99732843 -6.73746651
Axis -0.34843160 -0.87713170 -0.33050779
Axis point 111.08779067 0.00000000 125.00746186
Rotation angle (degrees) 4.43862291
Shift along axis -1.53648193
> vop add #7-9 onGrid #1
Opened volume sum as #10, grid size 480,480,480, pixel 0.824, shown at step 1,
values float32
> save
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/female_mutant/class_245/new_maps/rps9_fmt_FR_combined_aligned2shiny_with_antiibiotic_p824_class245_with_blush.mrc
> models #10
> save
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/female_mutant/class_245/new_maps/rps9_fmt_shiny_with_antiibiotic_p824_class245_with_blush.mrc
> models #1
> close session
> open
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/Male_wildtype/class2_blush/maps/rps9_mwt_shiny_with_antiibiotic_p842_class2_with_blush.mrc
Opened rps9_mwt_shiny_with_antiibiotic_p842_class2_with_blush.mrc as #1, grid
size 480,480,480, pixel 0.85, shown at level 0.0203, step 2, values float32
> ui tool show "Map Coordinates"
> open
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/Male_wildtype/class2_blush/maps/rps9_mwt_FR_combined_aligned2shiny_with_antiibiotic_p842_class2_with_blush.mrc
Opened
rps9_mwt_FR_combined_aligned2shiny_with_antiibiotic_p842_class2_with_blush.mrc
as #2, grid size 480,480,480, pixel 0.85, shown at level 0.0295, step 2,
values float32
> open
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/Male_wildtype/class2_blush/maps/rps9_mwt_multibody_combined_aligned2shiny_with_antiibiotic_p842_class2_with_blush.mrc
Opened
rps9_mwt_multibody_combined_aligned2shiny_with_antiibiotic_p842_class2_with_blush.mrc
as #3, grid size 480,480,480, pixel 0.85, shown at level 0.026, step 2, values
float32
> close #2
> close #3
> open
> /archive/processing/disha/RPS9_male_control_p3/relion/MultiBody/Multibody_class2/run_body001.mrc
> /archive/processing/disha/RPS9_male_control_p3/relion/MultiBody/Multibody_class2/run_body002.mrc
> /archive/processing/disha/RPS9_male_control_p3/relion/MultiBody/Multibody_class2/run_body003.mrc
Opened run_body001.mrc as #2.1, grid size 480,480,480, pixel 0.85, shown at
level 0.018, step 2, values float32
Opened run_body002.mrc as #2.2, grid size 480,480,480, pixel 0.85, shown at
level 0.00937, step 2, values float32
Opened run_body003.mrc as #2.3, grid size 480,480,480, pixel 0.85, shown at
level 0.00565, step 2, values float32
> ui tool show "Fit in Map"
> fitmap #2.1 inMap #1
Fit map run_body001.mrc in map
rps9_mwt_shiny_with_antiibiotic_p842_class2_with_blush.mrc using 138070 points
correlation = 0.9952, correlation about mean = 0.9096, overlap = 89.42
steps = 80, shift = 0.244, angle = 3.09 degrees
Position of run_body001.mrc (#2.1) relative to
rps9_mwt_shiny_with_antiibiotic_p842_class2_with_blush.mrc (#1) coordinates:
Matrix rotation and translation
0.99905587 -0.03763981 -0.02169362 11.44535865
0.03692564 0.99879162 -0.03243138 -1.06078430
0.02288812 0.03159970 0.99923851 -10.42152275
Axis 0.59329974 -0.41308590 0.69090915
Axis point 38.31457570 302.66721101 0.00000000
Rotation angle (degrees) 3.09328759
Shift along axis 0.02839790
> fitmap #2.2 inMap #1
Fit map run_body002.mrc in map
rps9_mwt_shiny_with_antiibiotic_p842_class2_with_blush.mrc using 138103 points
correlation = 0.9849, correlation about mean = 0.8346, overlap = 32.87
steps = 92, shift = 0.761, angle = 2.61 degrees
Position of run_body002.mrc (#2.2) relative to
rps9_mwt_shiny_with_antiibiotic_p842_class2_with_blush.mrc (#1) coordinates:
Matrix rotation and translation
0.99949182 0.02208707 0.02298414 -8.60914355
-0.02282069 0.99922212 0.03216151 0.16424606
-0.02225591 -0.03266968 0.99921838 12.87753944
Axis -0.71305728 0.49758070 -0.49392587
Axis point 0.00000000 392.00439514 2.20815429
Rotation angle (degrees) 2.60556498
Shift along axis -0.14001165
> fitmap #2.3 inMap #1
Fit map run_body003.mrc in map
rps9_mwt_shiny_with_antiibiotic_p842_class2_with_blush.mrc using 137948 points
correlation = 0.8973, correlation about mean = 0.4404, overlap = 20.75
steps = 76, shift = 0.389, angle = 1.95 degrees
Position of run_body003.mrc (#2.3) relative to
rps9_mwt_shiny_with_antiibiotic_p842_class2_with_blush.mrc (#1) coordinates:
Matrix rotation and translation
0.99992847 -0.01193505 -0.00078255 3.50004396
0.01190415 0.99942384 -0.03178492 1.85241158
0.00116145 0.03177333 0.99949443 -9.67895097
Axis 0.93592197 -0.02862613 0.35104218
Axis point 0.00000000 303.52908225 52.61995850
Rotation angle (degrees) 1.94584562
Shift along axis -0.17497943
> vop all level 0.009
> fitmap #2.3 inMap #1
Fit map run_body003.mrc in map
rps9_mwt_shiny_with_antiibiotic_p842_class2_with_blush.mrc using 60995 points
correlation = 0.9642, correlation about mean = 0.6769, overlap = 14.42
steps = 40, shift = 0.0332, angle = 0.144 degrees
Position of run_body003.mrc (#2.3) relative to
rps9_mwt_shiny_with_antiibiotic_p842_class2_with_blush.mrc (#1) coordinates:
Matrix rotation and translation
0.99993484 -0.01136190 0.00110666 3.08634991
0.01139247 0.99937945 -0.03333069 2.22556830
-0.00072727 0.03334113 0.99944377 -9.65960371
Axis 0.94607976 0.02602361 0.32288677
Axis point 0.00000000 289.37977334 61.49481437
Rotation angle (degrees) 2.01928249
Shift along axis -0.14110775
> vop resample #2 onGrid #1
Opened run_body001.mrc resampled as #3, grid size 480,480,480, pixel 0.842,
shown at step 1, values float32
Opened run_body002.mrc resampled as #4, grid size 480,480,480, pixel 0.842,
shown at step 1, values float32
Opened run_body003.mrc resampled as #5, grid size 480,480,480, pixel 0.842,
shown at step 1, values float32
> vop add #3-5 onGrid #1
Opened volume sum as #6, grid size 480,480,480, pixel 0.842, shown at step 1,
values float32
> save
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/Male_wildtype/class2_blush/maps/rps9_mwt_multibody_combined_aligned2shiny_with_antiibiotic_p842_class2_with_blush.mrc
> models #6
> save
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/Male_wildtype/class2_blush/maps/rps9_mwt_shiny_with_antiibiotic_p842_class2_with_blush.mrc
> models #1
> open
> /archive/processing/disha/RPS9_male_control_p3/relion/PostProcess/FR_40S_body_class2/postprocess_masked.mrc
Opened postprocess_masked.mrc as #7, grid size 480,480,480, pixel 0.842, shown
at level 0.00997, step 2, values float32
> open
> /archive/processing/disha/RPS9_male_control_p3/relion/PostProcess/FR_40S_head_class2/postprocess_masked.mrc
Opened postprocess_masked.mrc as #8, grid size 480,480,480, pixel 0.842, shown
at level 0.000738, step 2, values float32
> open
> /archive/processing/disha/RPS9_male_control_p3/relion/PostProcess/FR_60S_class2/postprocess_masked.mrc
Opened postprocess_masked.mrc as #9, grid size 480,480,480, pixel 0.842, shown
at level 0.0288, step 2, values float32
> vop all level 0.009
> fitmap #7 inMap #1
Fit map postprocess_masked.mrc in map
rps9_mwt_shiny_with_antiibiotic_p842_class2_with_blush.mrc using 154409 points
correlation = 0.9354, correlation about mean = 0.6771, overlap = 41.94
steps = 88, shift = 0.645, angle = 2.48 degrees
Position of postprocess_masked.mrc (#7) relative to
rps9_mwt_shiny_with_antiibiotic_p842_class2_with_blush.mrc (#1) coordinates:
Matrix rotation and translation
0.99957862 0.01975102 0.02127159 -7.78918899
-0.02042501 0.99928081 0.03194805 -0.31933719
-0.02062529 -0.03236906 0.99926315 12.45519776
Axis -0.74236561 0.48358520 -0.46372261
Axis point 0.00000000 382.29780120 16.36493667
Rotation angle (degrees) 2.48277432
Shift along axis -0.14775755
> fitmap #8 inMap #1
Fit map postprocess_masked.mrc in map
rps9_mwt_shiny_with_antiibiotic_p842_class2_with_blush.mrc using 66938 points
correlation = 0.9161, correlation about mean = 0.659, overlap = 19.97
steps = 60, shift = 0.341, angle = 1.85 degrees
Position of postprocess_masked.mrc (#8) relative to
rps9_mwt_shiny_with_antiibiotic_p842_class2_with_blush.mrc (#1) coordinates:
Matrix rotation and translation
0.99994379 -0.01060202 -0.00006877 2.98639379
0.01059500 0.99947948 -0.03047155 1.98549081
0.00039179 0.03046911 0.99953563 -9.06499708
Axis 0.94447148 -0.00713781 0.32851587
Axis point 0.00000000 296.57935724 60.05242107
Rotation angle (degrees) 1.84878459
Shift along axis -0.17160369
> fitmap #9 inMap #1
Fit map postprocess_masked.mrc in map
rps9_mwt_shiny_with_antiibiotic_p842_class2_with_blush.mrc using 510793 points
correlation = 0.9177, correlation about mean = 0.7241, overlap = 231.4
steps = 84, shift = 0.379, angle = 3.09 degrees
Position of postprocess_masked.mrc (#9) relative to
rps9_mwt_shiny_with_antiibiotic_p842_class2_with_blush.mrc (#1) coordinates:
Matrix rotation and translation
0.99906112 -0.03751837 -0.02166204 11.42810771
0.03680534 0.99879622 -0.03242641 -1.03279841
0.02285255 0.03159868 0.99923935 -10.41788970
Axis 0.59433575 -0.41322255 0.68993633
Axis point 37.62596132 303.16408288 0.00000000
Rotation angle (degrees) 3.08760118
Shift along axis 0.03122801
> vop add #7-9 onGrid #1
Opened volume sum as #10, grid size 480,480,480, pixel 0.842, shown at step 1,
values float32
> hide #!6 models
> hide #!1 models
> show #!1 models
No map chosen to save
> save
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/Male_wildtype/class2_blush/maps/rps9_mwt_FR_combined_aligned2shiny_with_antiibiotic_p842_class2_with_blush.mrc
> models #10
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> close session
> open
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/Male_wildtype/class3_blush/maps/rps9_mwt_multibody_combined_aligned2shiny_with_antiibiotic_p842_class3_with_blush_EMReady.mrc
Opened
rps9_mwt_multibody_combined_aligned2shiny_with_antiibiotic_p842_class3_with_blush_EMReady.mrc
as #1, grid size 480,480,480, pixel 0.842, shown at level 7.58, step 2, values
float32
> vop all level 0.009
> vop all level 0.03
> vop all level 0.05
> volume #1 step 1
> volume #1 level 3.948
> open
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/Male_wildtype/new_merged_male_WT-
> coot-5.pdb
Chain information for new_merged_male_WT-coot-5.pdb #2
---
Chain | Description
L5 | No description available
L7 | No description available
L8 | No description available
LA | No description available
LB | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
Le | No description available
Lf | No description available
Lj | No description available
S2 | No description available
S6 | No description available
SA | No description available
SB | No description available
SC | No description available
SD | No description available
SF | No description available
SG | No description available
SH | No description available
SI | No description available
SJ | No description available
SK | No description available
SL | No description available
SO | No description available
SP | No description available
SQ | No description available
SR | No description available
SS | No description available
ST | No description available
SU | No description available
SV | No description available
SW | No description available
SX | No description available
SZ | No description available
Sa | No description available
Sb | No description available
Sc | No description available
Se | No description available
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule new_merged_male_WT-coot-5.pdb (#2) to map
rps9_mwt_multibody_combined_aligned2shiny_with_antiibiotic_p842_class3_with_blush_EMReady.mrc
(#1) using 174882 atoms
average map value = 7.604, steps = 72
shifted from previous position = 4.53
rotated from previous position = 1.12 degrees
atoms outside contour = 55661, contour level = 3.9479
Position of new_merged_male_WT-coot-5.pdb (#2) relative to
rps9_mwt_multibody_combined_aligned2shiny_with_antiibiotic_p842_class3_with_blush_EMReady.mrc
(#1) coordinates:
Matrix rotation and translation
0.99983081 0.01836333 0.00106635 -5.29551370
-0.01837008 0.99980876 0.00670771 0.09328388
-0.00094297 -0.00672617 0.99997693 5.34522442
Axis -0.34301246 0.05130468 -0.93792872
Axis point 10.36947031 348.09810587 0.00000000
Rotation angle (degrees) 1.12204913
Shift along axis -3.19222638
> save
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/Male_wildtype/class3_blush/models/rps9_mwt_multibody_combined_aligned2shiny_with_antiibiotic_p842_class3_with_blush_EMReady.pdb
> relModel #1
> close session
> open
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/female_mutant/class_245/new_maps/rps9_fmt_multibody_combined_aligned2shiny_with_antiibiotic_p824_class245_with_blush.mrc
Opened
rps9_fmt_multibody_combined_aligned2shiny_with_antiibiotic_p824_class245_with_blush.mrc
as #1, grid size 480,480,480, pixel 0.824, shown at level 0.0135, step 2,
values float32
> close session
> open
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/female_mutant/class_245/new_maps/rps9_fmt_shiny_with_antiibiotic_p824_class245_with_blush.mrc
Opened rps9_fmt_shiny_with_antiibiotic_p824_class245_with_blush.mrc as #1,
grid size 480,480,480, pixel 0.824, shown at level 0.011, step 2, values
float32
> vop all level 0.009\
> volume all level 0.009\
Invalid "level" argument: Expected a number
> vop all level 0.009\
> volume all level 0.009\
Invalid "level" argument: Expected a number
> vop all level 0.009
> vop all level 0.005
> open
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/female_mutant/class_245/few_female_mt_class245_aln-
> coot-2.pdb
Summary of feedback from opening
/yonath_group/disha/RPS9_liver/new_maps_models_p824/female_mutant/class_245/few_female_mt_class245_aln-
coot-2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ALA C 26
LYS C 29 1 4
Start residue of secondary structure not found: HELIX 2 2 PRO C 34 LEU C 44 1
11
Start residue of secondary structure not found: HELIX 3 3 THR C 117 LEU C 128
1 12
Start residue of secondary structure not found: HELIX 4 4 ALA C 129 ALA C 132
1 4
Start residue of secondary structure not found: HELIX 5 5 PRO C 134 VAL C 137
1 4
639 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (34 )
Cannot find LINK/SSBOND residue CYS (12 )
Cannot find LINK/SSBOND residue CYS (15 )
Cannot find LINK/SSBOND residue CYS (72 )
Cannot find LINK/SSBOND residue CYS (77 )
22 messages similar to the above omitted
Chain information for few_female_mt_class245_aln-coot-2.pdb #2
---
Chain | Description
2 | No description available
C | No description available
J | No description available
L5 | No description available
L7 | No description available
L8 | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
LQ | No description available
LR | No description available
LS | No description available
LT | No description available
LU | No description available
LV | No description available
LW | No description available
LX | No description available
LY | No description available
LZ | No description available
La | No description available
Lb | No description available
Lc | No description available
Ld | No description available
Le | No description available
Lf | No description available
Lg | No description available
Lh | No description available
Li | No description available
Lj | No description available
Lk | No description available
Ll | No description available
Lm | No description available
Ln | No description available
Lo | No description available
Lp | No description available
Lr | No description available
R | No description available
SD | No description available
SE | No description available
SF | No description available
SG | No description available
SH | No description available
SI | No description available
SK | No description available
SL | No description available
SN | No description available
SO | No description available
SP | No description available
SQ | No description available
SR | No description available
SS | No description available
ST | No description available
SU | No description available
SV | No description available
SW | No description available
SX | No description available
SY | No description available
SZ | No description available
Sa | No description available
Sb | No description available
Sc | No description available
Sd | No description available
Se | No description available
Sg | No description available
t | No description available
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule few_female_mt_class245_aln-coot-2.pdb (#2) to map
rps9_fmt_shiny_with_antiibiotic_p824_class245_with_blush.mrc (#1) using 208034
atoms
average map value = 0.01099, steps = 64
shifted from previous position = 1.55
rotated from previous position = 1.78 degrees
atoms outside contour = 11893, contour level = 0.005
Position of few_female_mt_class245_aln-coot-2.pdb (#2) relative to
rps9_fmt_shiny_with_antiibiotic_p824_class245_with_blush.mrc (#1) coordinates:
Matrix rotation and translation
0.99993661 0.00801230 -0.00791100 -0.86058682
-0.00778056 0.99955199 0.02890141 -2.98782259
0.00813902 -0.02883802 0.99955096 5.14930943
Axis -0.93166184 -0.25897707 -0.25482759
Axis point 0.00000000 179.27070382 103.79882812
Rotation angle (degrees) 1.77572774
Shift along axis 0.26336733
> ui tool show "Map Coordinates"
> open
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/female_mutant/class_245/phenix/RealSpaceRefine_2/RPS9_FMT_Class245_real_space_refined_002-coot-0.pdb
Summary of feedback from opening
/yonath_group/disha/RPS9_liver/new_maps_models_p824/female_mutant/class_245/phenix/RealSpaceRefine_2/RPS9_FMT_Class245_real_space_refined_002-coot-0.pdb
---
warnings | Ignored bad PDB record found on line 788
SSBOND 1 CYS Sg 153 CYS Sg 168
Ignored bad PDB record found on line 789
SSBOND 2 CYS Sg 240 CYS Sg 249
Start residue of secondary structure not found: HELIX 1 1 ILE A 5 GLY A 13 1 9
Start residue of secondary structure not found: HELIX 2 2 ASP A 33 HIS A 38 1
6
Start residue of secondary structure not found: HELIX 3 3 PRO A 103 PRO A 108
1 6
Start residue of secondary structure not found: HELIX 4 4 LYS A 181 ARG A 193
1 13
Start residue of secondary structure not found: HELIX 5 5 ARG A 200 ASN A 205
1 6
701 messages similar to the above omitted
Cannot find LINK/SSBOND residue ZN (201 )
Cannot find LINK/SSBOND residue ZN (201 )
Cannot find LINK/SSBOND residue ZN (201 )
Cannot find LINK/SSBOND residue ZN (201 )
Cannot find LINK/SSBOND residue ZN (101 )
22 messages similar to the above omitted
Chain information for RPS9_FMT_Class245_real_space_refined_002-coot-0.pdb #3
---
Chain | Description
L5 | No description available
L7 | No description available
L8 | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
LQ | No description available
LR | No description available
LS | No description available
LT | No description available
LU | No description available
LV | No description available
LW | No description available
LX | No description available
LY | No description available
LZ | No description available
La | No description available
Lb | No description available
Lc | No description available
Ld | No description available
Le | No description available
Lf | No description available
Lg | No description available
Lh | No description available
Li | No description available
Lj | No description available
Lk | No description available
Ll | No description available
Lm | No description available
Ln | No description available
Lo | No description available
Lp | No description available
Lr | No description available
Pt | No description available
S2 | No description available
SC | No description available
SD | No description available
SE | No description available
SF | No description available
SG | No description available
SH | No description available
SI | No description available
SJ | No description available
SK | No description available
SL | No description available
SN | No description available
SO | No description available
SP | No description available
SQ | No description available
SR | No description available
SS | No description available
ST | No description available
SU | No description available
SV | No description available
SW | No description available
SX | No description available
SY | No description available
SZ | No description available
Sa | No description available
Sb | No description available
Sc | No description available
Sd | No description available
Se | No description available
Sg | No description available
mR | No description available
t | No description available
> hide #!2 models
> fitmap #3 inMap #1
Fit molecule RPS9_FMT_Class245_real_space_refined_002-coot-0.pdb (#3) to map
rps9_fmt_shiny_with_antiibiotic_p824_class245_with_blush.mrc (#1) using 208034
atoms
average map value = 0.01117, steps = 68
shifted from previous position = 1.52
rotated from previous position = 1.77 degrees
atoms outside contour = 9947, contour level = 0.005
Position of RPS9_FMT_Class245_real_space_refined_002-coot-0.pdb (#3) relative
to rps9_fmt_shiny_with_antiibiotic_p824_class245_with_blush.mrc (#1)
coordinates:
Matrix rotation and translation
0.99993728 0.00796157 -0.00787674 -0.85481870
-0.00773092 0.99955265 0.02889171 -3.00855389
0.00810324 -0.02882901 0.99955151 5.11122902
Axis -0.93227829 -0.25810134 -0.25345784
Axis point 0.00000000 178.11417631 104.40679899
Rotation angle (degrees) 1.77397789
Shift along axis 0.27795964
> save
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/female_mutant/class_245/models/RPS9_FMT_Class245_real_space_refined_002-coot-0.pdb
> models #3 relModel #1
> hide #!1 models
> open
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/Male_wildtype/class3_blush/models/rps9_mwt_multibody_combined_aligned2shiny_with_antiibiotic_p842_class3_with_blush_EMReady.pdb
Chain information for
rps9_mwt_multibody_combined_aligned2shiny_with_antiibiotic_p842_class3_with_blush_EMReady.pdb
#4
---
Chain | Description
L5 | No description available
L7 | No description available
L8 | No description available
LA | No description available
LB | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
Le | No description available
Lf | No description available
Lj | No description available
S2 | No description available
S6 | No description available
SA | No description available
SB | No description available
SC | No description available
SD | No description available
SF | No description available
SG | No description available
SH | No description available
SI | No description available
SJ | No description available
SK | No description available
SL | No description available
SO | No description available
SP | No description available
SQ | No description available
SR | No description available
SS | No description available
ST | No description available
SU | No description available
SV | No description available
SW | No description available
SX | No description available
SZ | No description available
Sa | No description available
Sb | No description available
Sc | No description available
Se | No description available
> ui tool show Matchmaker
> matchmaker #!4 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RPS9_FMT_Class245_real_space_refined_002-coot-0.pdb, chain L5 (#3)
with
rps9_mwt_multibody_combined_aligned2shiny_with_antiibiotic_p842_class3_with_blush_EMReady.pdb,
chain L5 (#4), sequence alignment score = 20827.3
RMSD between 3243 pruned atom pairs is 0.646 angstroms; (across all 3471
pairs: 1.407)
> hide #!3-4 cartoons
> show #!3-4 cartoons
> color #3 cyan
> color #4 magenta
> set bgColor white
> set bgColor #ffffff00
> hide #!3-4 atoms
> select #4/SJ
1544 atoms, 1565 bonds, 1 pseudobond, 188 residues, 2 models selected
> color (#!4 & sel) orange
> select clear
> show #!1 models
> transparency 50
> hide #!4 models
> show #!4 models
> hide #!1 models
> open
> /yonath_group/disha/RPS26/models_maps/Mutant_TISU/Class1_tRNA/Phenix/RealSpaceRefine_14/rps26_mutant_TISU_real_space_refined_014.cif
Summary of feedback from opening
/yonath_group/disha/RPS26/models_maps/Mutant_TISU/Class1_tRNA/Phenix/RealSpaceRefine_14/rps26_mutant_TISU_real_space_refined_014.cif
---
warnings | Skipping chem_comp category: Missing column 'type' near line 4372
Missing entity information. Treating each chain as a separate entity.
Expected gap or linking atom in HY3 /SX:62 for GLN /SX:61
Missing or incomplete sequence information. Inferred polymer connectivity.
Skipping chem_comp category: Missing column 'type' near line 204449
Skipping chem_comp category: Missing column 'type' near line 204476
Skipping chem_comp category: Missing column 'type' near line 204625
Skipping chem_comp category: Missing column 'type' near line 204652
Skipping chem_comp category: Missing column 'type' near line 204913
22 messages similar to the above omitted
Chain information for rps26_mutant_TISU_real_space_refined_014.cif #5
---
Chain | Description
L5 | No description available
L7 | No description available
L8 | No description available
LA | No description available
LB | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
LQ | No description available
LR | No description available
LS | No description available
LT | No description available
LU | No description available
LV | No description available
LW | No description available
LX | No description available
LY | No description available
LZ | No description available
La | No description available
Lb | No description available
Lc | No description available
Ld | No description available
Le | No description available
Lf | No description available
Lg | No description available
Lh | No description available
Li | No description available
Lj | No description available
Lk | No description available
Ll | No description available
Lm | No description available
Ln | No description available
Lo | No description available
Lp | No description available
Lr | No description available
Pt | No description available
S2 | No description available
SA | No description available
SB | No description available
SC | No description available
SD | No description available
SE | No description available
SF | No description available
SG | No description available
SH | No description available
SI | No description available
SJ | No description available
SK | No description available
SL | No description available
SN | No description available
SO | No description available
SP | No description available
SQ | No description available
SR | No description available
SS | No description available
ST | No description available
SU | No description available
SV | No description available
SW | No description available
SX | No description available
SY | No description available
SZ | No description available
Sa | No description available
Sb | No description available
Sc | No description available
Sd | No description available
Se | No description available
Sg | No description available
mR | No description available
> ui tool show Matchmaker
> matchmaker #!5 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker RPS9_FMT_Class245_real_space_refined_002-coot-0.pdb, chain L5 (#3)
with rps26_mutant_TISU_real_space_refined_014.cif, chain L5 (#5), sequence
alignment score = 19715.6
RMSD between 3038 pruned atom pairs is 0.617 angstroms; (across all 3365
pairs: 3.417)
> show #!1 models
> open
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/miriam/female_mutant/class1/models/RPS9_FMT_class1_real_space_refined_004_MW_14_8_24.cif
Summary of feedback from opening
/yonath_group/disha/RPS9_liver/new_maps_models_p824/miriam/female_mutant/class1/models/RPS9_FMT_class1_real_space_refined_004_MW_14_8_24.cif
---
warnings | Unknown polymer entity '1' near line 52
Expected gap or connection between A /Pt:77 and MET /Pt:78
Atom O1P is not in the residue template for C /L5:172
Atom O1P is not in the residue template for C /L5:174
Atom O1P is not in the residue template for C /L5:183
Atom O1P is not in the residue template for U /L5:184
Atom O1P is not in the residue template for C /L5:185
8 messages similar to the above omitted
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for RPS9_FMT_class1_real_space_refined_004_MW_14_8_24.cif #6
---
Chain | Description
At | No description available
L5 | No description available
L7 | No description available
L8 | No description available
LA | No description available
LB | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
LQ | No description available
LR | No description available
LS | No description available
LT | No description available
LV | No description available
LW | No description available
LX | No description available
LY | No description available
LZ | No description available
La | No description available
Lb | No description available
Lc | No description available
Ld | No description available
Le | No description available
Lf | No description available
Lg | No description available
Lh | No description available
Li | No description available
Lj | No description available
Lk | No description available
Ll | No description available
Ln | No description available
Lo | No description available
Lr | No description available
Pt | No description available
S2 | No description available
SA | No description available
SB | No description available
SC | No description available
SD | No description available
SE | No description available
SF | No description available
SG | No description available
SI | No description available
SJ | No description available
SL | No description available
SN | No description available
SO | No description available
SP | No description available
SQ | No description available
SR | No description available
SS | No description available
ST | No description available
SU | No description available
SV | No description available
SW | No description available
SX | No description available
SY | No description available
SZ | No description available
Sa | No description available
Sb | No description available
Sc | No description available
Sd | No description available
Se | No description available
mR | No description available
> ui tool show Matchmaker
> matchmaker #!6 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
rps9_mwt_multibody_combined_aligned2shiny_with_antiibiotic_p842_class3_with_blush_EMReady.pdb,
chain L5 (#4) with RPS9_FMT_class1_real_space_refined_004_MW_14_8_24.cif,
chain L5 (#6), sequence alignment score = 19728.2
RMSD between 3103 pruned atom pairs is 0.592 angstroms; (across all 3321
pairs: 1.599)
> show #!3-6 cartoons
> hide #!3-6 atoms
> color #5 #ff5500ff
> color #6 #55ff7fff
> hide #!1 models
> hide #!5 models
> hide #!3 models
> ui tool show Matchmaker
> matchmaker #!5 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
rps9_mwt_multibody_combined_aligned2shiny_with_antiibiotic_p842_class3_with_blush_EMReady.pdb,
chain L5 (#4) with rps26_mutant_TISU_real_space_refined_014.cif, chain L5
(#5), sequence alignment score = 19431.3
RMSD between 2974 pruned atom pairs is 0.606 angstroms; (across all 3327
pairs: 3.362)
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!6 models
> color #5 #aaaaffff
> show #!6 models
> hide #!4 models
> show #!3 models
> show #!1 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> hide #!5 models
> show #!5 models
> show #!4 models
> hide #!6 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!6 models
> open
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/Male_wildtype/class2_blush/maps/rps9_mwt_shiny_with_antiibiotic_p842_class2_with_blush.mrc
Opened rps9_mwt_shiny_with_antiibiotic_p842_class2_with_blush.mrc as #7, grid
size 480,480,480, pixel 0.842, shown at level 0.0203, step 2, values float32
> hide #!4 models
> hide #!5 models
> hide #!6 models
> open
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/Male_wildtype/new_merged_male_WT-
> coot-5.pdb
Chain information for new_merged_male_WT-coot-5.pdb #8
---
Chain | Description
L5 | No description available
L7 | No description available
L8 | No description available
LA | No description available
LB | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
Le | No description available
Lf | No description available
Lj | No description available
S2 | No description available
S6 | No description available
SA | No description available
SB | No description available
SC | No description available
SD | No description available
SF | No description available
SG | No description available
SH | No description available
SI | No description available
SJ | No description available
SK | No description available
SL | No description available
SO | No description available
SP | No description available
SQ | No description available
SR | No description available
SS | No description available
ST | No description available
SU | No description available
SV | No description available
SW | No description available
SX | No description available
SZ | No description available
Sa | No description available
Sb | No description available
Sc | No description available
Se | No description available
> volume #7 level 0.005
> volume #7 color #aaffff
> volume #7 color #7dbcbc
> fitmap #8 inMap #7
Fit molecule new_merged_male_WT-coot-5.pdb (#8) to map
rps9_mwt_shiny_with_antiibiotic_p842_class2_with_blush.mrc (#7) using 174882
atoms
average map value = 0.01812, steps = 104
shifted from previous position = 4.95
rotated from previous position = 1.49 degrees
atoms outside contour = 6430, contour level = 0.005
Position of new_merged_male_WT-coot-5.pdb (#8) relative to
rps9_mwt_shiny_with_antiibiotic_p842_class2_with_blush.mrc (#7) coordinates:
Matrix rotation and translation
0.99967921 0.02095305 0.01422816 -8.40526105
-0.02103547 0.99976266 0.00566807 0.50442168
-0.01410602 -0.00596555 0.99988271 8.06496244
Axis -0.22383914 0.54517004 -0.80788964
Axis point 131.88083203 449.73499176 0.00000000
Rotation angle (degrees) 1.48908723
Shift along axis -4.35917761
> volume #7 level 0.009
> open
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/female_mutant/class_245/models/RPS9_FMT_Class245_real_space_refined_002-coot-0.pdb
Chain information for RPS9_FMT_Class245_real_space_refined_002-coot-0.pdb #9
---
Chain | Description
A | No description available
B | No description available
L5 | No description available
L7 | No description available
L8 | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
LQ | No description available
LR | No description available
LS | No description available
LT | No description available
LU | No description available
LV | No description available
LW | No description available
LX | No description available
LY | No description available
LZ | No description available
La | No description available
Lb | No description available
Lc | No description available
Ld | No description available
Le | No description available
Lf | No description available
Lg | No description available
Lh | No description available
Li | No description available
Lj | No description available
Lk | No description available
Ll | No description available
Lm | No description available
Ln | No description available
Lo | No description available
Lp | No description available
Lr | No description available
Pt | No description available
S2 | No description available
SC | No description available
SD | No description available
SE | No description available
SF | No description available
SG | No description available
SH | No description available
SI | No description available
SJ | No description available
SK | No description available
SL | No description available
SN | No description available
SO | No description available
SP | No description available
SQ | No description available
SR | No description available
SS | No description available
ST | No description available
SU | No description available
SV | No description available
SW | No description available
SX | No description available
SY | No description available
SZ | No description available
Sa | No description available
Sb | No description available
Sc | No description available
Sd | No description available
Se | No description available
Sg | No description available
mR | No description available
t | No description available
> ui tool show Matchmaker
> matchmaker #!9 to #8
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker new_merged_male_WT-coot-5.pdb, chain L5 (#8) with
RPS9_FMT_Class245_real_space_refined_002-coot-0.pdb, chain L5 (#9), sequence
alignment score = 20827.3
RMSD between 3243 pruned atom pairs is 0.646 angstroms; (across all 3471
pairs: 1.407)
> fitmap #9 inMap #7
Fit molecule RPS9_FMT_Class245_real_space_refined_002-coot-0.pdb (#9) to map
rps9_mwt_shiny_with_antiibiotic_p842_class2_with_blush.mrc (#7) using 208034
atoms
average map value = 0.01756, steps = 84
shifted from previous position = 0.0446
rotated from previous position = 0.0363 degrees
atoms outside contour = 32160, contour level = 0.009
Position of RPS9_FMT_Class245_real_space_refined_002-coot-0.pdb (#9) relative
to rps9_mwt_shiny_with_antiibiotic_p842_class2_with_blush.mrc (#7)
coordinates:
Matrix rotation and translation
-0.69439714 -0.59465211 0.40521782 374.52087770
0.32667009 -0.76225212 -0.55880083 412.00907175
0.64117023 -0.25565715 0.72356075 -36.89371941
Axis 0.30369017 -0.23637777 0.92298311
Axis point 134.25569513 256.30930597 0.00000000
Rotation angle (degrees) 150.05950930
Shift along axis -17.70375872
> close #9
> open
> /yonath_group/disha/RPS9_liver/new_maps_models_p824/female_mutant/class1/phenix/RealSpaceRefine_4/RPS9_FMT_class1_real_space_refined_004.cif
Summary of feedback from opening
/yonath_group/disha/RPS9_liver/new_maps_models_p824/female_mutant/class1/phenix/RealSpaceRefine_4/RPS9_FMT_class1_real_space_refined_004.cif
---
warnings | Skipping chem_comp category: Missing column 'type' near line 5897
Missing entity information. Treating each chain as a separate entity.
Invalid residue range for struct_conf "1": invalid chain "LO", near line 175
Invalid residue range for struct_conf "2": invalid chain "LO", near line 176
Invalid residue range for struct_conf "3": invalid chain "LO", near line 177
Invalid residue range for struct_conf "4": invalid chain "LO", near line 178
Invalid residue range for struct_conf "5": invalid chain "LO", near line 179
261 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "1 1": invalid chain "LO", near
line 5720
Invalid sheet range for struct_sheet_range "2 1": invalid chain "LO", near
line 5721
Invalid sheet range for struct_sheet_range "3 1": invalid chain "LO", near
line 5722
Invalid sheet range for struct_sheet_range "4 1": invalid chain "LO", near
line 5723
Invalid sheet range for struct_sheet_range "5 1": invalid chain "LO", near
line 5724
171 messages similar to the above omitted
Missing or incomplete sequence information. Inferred polymer connectivity.
Skipping chem_comp category: Missing column 'type' near line 175137
Skipping chem_comp category: Missing column 'type' near line 175422
Skipping chem_comp category: Missing column 'type' near line 175701
Skipping chem_comp category: Missing column 'type' near line 175962
Skipping chem_comp category: Missing column 'type' near line 176214
6 messages similar to the above omitted
Chain information for RPS9_FMT_class1_real_space_refined_004.cif #9
---
Chain | Description
At | No description available
L5 | No description available
L7 | No description available
L8 | No description available
LA | No description available
LB | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
Le | No description available
Lf | No description available
Lj | No description available
Pt | No description available
S2 | No description available
SB | No description available
SC | No description available
SD | No description available
SE | No description available
SF | No description available
SI | No description available
SJ | No description available
SL | No description available
SO | No description available
SP | No description available
SR | No description available
SS | No description available
ST | No description available
SV | No description available
SW | No description available
SX | No description available
SZ | No description available
Sb | No description available
Se | No description available
mR | No description available
> ui tool show Matchmaker
> matchmaker #!9 to #8
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker new_merged_male_WT-coot-5.pdb, chain L5 (#8) with
RPS9_FMT_class1_real_space_refined_004.cif, chain L5 (#9), sequence alignment
score = 21009.3
RMSD between 3408 pruned atom pairs is 0.639 angstroms; (across all 3471
pairs: 0.733)
> hide #!7 models
> hide #!8 models
> hide #!9 models
> show #!6 models
> show #!5 models
> show #!3 models
> show #!4 models
> hide #!6 models
> close session
> open
> /archive/processing/disha/20230211_female_wildtype_rps9/relion/Class3D/3d_class_again/run_it010_class001.mrc
> /archive/processing/disha/20230211_female_wildtype_rps9/relion/Class3D/3d_class_again/run_it010_class002.mrc
> /archive/processing/disha/20230211_female_wildtype_rps9/relion/Class3D/3d_class_again/run_it010_class003.mrc
> /archive/processing/disha/20230211_female_wildtype_rps9/relion/Class3D/3d_class_again/run_it010_class004.mrc
> /archive/processing/disha/20230211_female_wildtype_rps9/relion/Class3D/3d_class_again/run_it010_class005.mrc
Opened run_it010_class001.mrc as #1.1, grid size 480,480,480, pixel 0.826,
shown at level 0.0041, step 2, values float32
Opened run_it010_class002.mrc as #1.2, grid size 480,480,480, pixel 0.826,
shown at level 0.00433, step 2, values float32
Opened run_it010_class003.mrc as #1.3, grid size 480,480,480, pixel 0.826,
shown at level 0.0035, step 2, values float32
Opened run_it010_class004.mrc as #1.4, grid size 480,480,480, pixel 0.826,
shown at level 0.00435, step 2, values float32
Opened run_it010_class005.mrc as #1.5, grid size 480,480,480, pixel 0.826,
shown at level 0.00689, step 2, values float32
> vop all level 0.005
> hide #!1.4 models
> show #!1.4 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.5 models
> hide #!1.1 models
> show #!1.1 models
> volume #1.1 level 0.001056
> hide #!1.1 models
> hide #!1.2 models
> hide #!1.3 models
> hide #!1.4 models
> show #!1.3 models
> show #!1.2 models
> volume #1.2 level 0.001939
> show #!1.4 models
> hide #!1.3 models
> hide #!1.2 models
> hide #!1.4 models
> close session
> open
> /archive/processing/disha/delta266/relion/InitialModel/3d_initial_model/run_it150_class001.mrc
Opened run_it150_class001.mrc as #1, grid size 110,110,110, pixel 3.4, shown
at level 0.0988, step 1, values float32
> volume #1 level 0.02527
[Repeated 1 time(s)]
> close session
> open
> /archive/processing/disha/20230211_female_wildtype_rps9/relion/Class3D/3d_class_again/run_it025_class001.mrc
> /archive/processing/disha/20230211_female_wildtype_rps9/relion/Class3D/3d_class_again/run_it025_class002.mrc
> /archive/processing/disha/20230211_female_wildtype_rps9/relion/Class3D/3d_class_again/run_it025_class003.mrc
> /archive/processing/disha/20230211_female_wildtype_rps9/relion/Class3D/3d_class_again/run_it025_class004.mrc
> /archive/processing/disha/20230211_female_wildtype_rps9/relion/Class3D/3d_class_again/run_it025_class005.mrc
Opened run_it025_class001.mrc as #1.1, grid size 480,480,480, pixel 0.826,
shown at level 0.00421, step 2, values float32
Opened run_it025_class002.mrc as #1.2, grid size 480,480,480, pixel 0.826,
shown at level 0.00443, step 2, values float32
Opened run_it025_class003.mrc as #1.3, grid size 480,480,480, pixel 0.826,
shown at level 0.00375, step 2, values float32
Opened run_it025_class004.mrc as #1.4, grid size 480,480,480, pixel 0.826,
shown at level 0.00452, step 2, values float32
Opened run_it025_class005.mrc as #1.5, grid size 480,480,480, pixel 0.826,
shown at level 0.00801, step 2, values float32
> vop all level 0.005
> hide #!1.1 models
> hide #!1.2 models
> hide #!1.3 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> vop all level 0.003
> hide #!1.5 models
> show #!1.4 models
> show #!1.3 models
> hide #!1.4 models
> volume #1.3 level 0.001336
> volume #1.4 level 0.001551
> hide #!1.3 models
> volume #1.2 level 0.001717
> hide #!1.4 models
> show #!1.1 models
> hide #!1.2 models
> volume #1.1 level 0.001293
> show #!1.2 models
> show #!1.3 models
> hide #!1.2 models
> hide #!1.1 models
> show #!1.4 models
> hide #!1.3 models
> show #!1.3 models
> hide #!1.4 models
> close session
> open
> /archive/processing/disha/20230211_female_wildtype_rps9/relion/Refine3D/3d_ref_shiny_class1/run_class001.mrc
Opened run_class001.mrc as #1, grid size 480,480,480, pixel 0.819, shown at
level 0.00708, step 2, values float32
> open
> /archive/processing/disha/20230211_female_wildtype_rps9/relion/Refine3D/3d_ref_shiny_class2/run_class001.mrc
Opened run_class001.mrc as #2, grid size 480,480,480, pixel 0.819, shown at
level 0.00697, step 2, values float32
> vop all level 0.003
Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 2 maps.
> surface dust #1 size 8.19
> surface dust #2 size 8.19
> ui tool show "Fit in Map"
> fitmap #1 inMap #2
Fit map run_class001.mrc in map run_class001.mrc using 458548 points
correlation = 0.8495, correlation about mean = 0.6746, overlap = 15.99
steps = 120, shift = 0.599, angle = 2.51 degrees
Position of run_class001.mrc (#1) relative to run_class001.mrc (#2)
coordinates:
Matrix rotation and translation
0.99907524 -0.03768939 -0.02069262 11.68793642
0.03751997 0.99925959 -0.00851595 -6.19381869
0.02099826 0.00773169 0.99974962 -5.75829310
Axis 0.18565936 -0.47639518 0.85940575
Axis point 168.91824603 305.12031410 0.00000000
Rotation angle (degrees) 2.50786955
Shift along axis 0.17196998
> vop all level 0.001
> vop all level 0.002
> close session
> open
> /archive/processing/disha/20230211_female_wildtype_rps9/relion/Refine3D/3d_ref_shiny/run_class001.mrc
Opened run_class001.mrc as #1, grid size 480,480,480, pixel 0.819, shown at
level 0.00745, step 2, values float32
> vop all level 0.005
> vop all level 0.002
> surface dust #1 size 8.19
> close session
> open
> /archive/processing/disha/20230211_female_wildtype_rps9/relion/Refine3D/3d_ref_shiny_again/run_class001.mrc
Opened run_class001.mrc as #1, grid size 480,480,480, pixel 0.819, shown at
level 0.00575, step 2, values float32
> vop all level 0.002
> surface dust #1 size 8.19
> volume #1 level 0.001
> close session
> open
> /yonath_group/disha/RPS26/models_maps/Control_Kozak/new_tRNA_maps/maps/60s_40s_multibody_aligned2shiny_kozak_control_tRNA_with_blush_inverted_again_EMready.mrc
Opened
60s_40s_multibody_aligned2shiny_kozak_control_tRNA_with_blush_inverted_again_EMready.mrc
as #1, grid size 480,480,480, pixel 0.842, shown at level 7.49, step 2, values
float32
> vop all level 0.005
> open
> /yonath_group/disha/RPS26/models_maps/Control_Kozak/new_tRNA_maps/models/Phenix/RealSpaceRefine_18/rps26_kozak_control_real_space_refined_018.eff
Unrecognized file suffix '.eff'
> open
> /yonath_group/disha/RPS26/models_maps/Control_Kozak/new_tRNA_maps/models/Phenix/RealSpaceRefine_18/rps26_kozak_control_real_space_refined_018.cif
Summary of feedback from opening
/yonath_group/disha/RPS26/models_maps/Control_Kozak/new_tRNA_maps/models/Phenix/RealSpaceRefine_18/rps26_kozak_control_real_space_refined_018.cif
---
warnings | Skipping chem_comp category: Missing column 'type' near line 9164
Missing entity information. Treating each chain as a separate entity.
Invalid residue range for struct_conf "1": invalid chain "SP", near line 202
Invalid residue range for struct_conf "2": invalid chain "SP", near line 203
Invalid residue range for struct_conf "3": invalid chain "SP", near line 204
Invalid residue range for struct_conf "4": invalid chain "SP", near line 205
Invalid residue range for struct_conf "5": invalid chain "SP", near line 206
352 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "1 1": invalid chain "SP", near
line 8587
Invalid sheet range for struct_sheet_range "1 2": invalid chain "SP", near
line 8588
Invalid sheet range for struct_sheet_range "1 3": invalid chain "SP", near
line 8589
Invalid sheet range for struct_sheet_range "2 1": invalid chain "LA", near
line 8590
Invalid sheet range for struct_sheet_range "2 2": invalid chain "LA", near
line 8591
341 messages similar to the above omitted
Missing or incomplete sequence information. Inferred polymer connectivity.
Skipping chem_comp category: Missing column 'type' near line 220218
Skipping chem_comp category: Missing column 'type' near line 220503
Skipping chem_comp category: Missing column 'type' near line 220782
Skipping chem_comp category: Missing column 'type' near line 221034
Skipping chem_comp category: Missing column 'type' near line 221275
21 messages similar to the above omitted
Chain information for rps26_kozak_control_real_space_refined_018.cif #2
---
Chain | Description
L5 | No description available
L7 | No description available
L8 | No description available
LA | No description available
LB | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
LQ | No description available
LR | No description available
LS | No description available
LT | No description available
LU | No description available
LV | No description available
LW | No description available
LX | No description available
LY | No description available
LZ | No description available
La | No description available
Lb | No description available
Lc | No description available
Ld | No description available
Le | No description available
Lf | No description available
Lg | No description available
Lh | No description available
Li | No description available
Lj | No description available
Lk | No description available
Ll | No description available
Lm | No description available
Ln | No description available
Lo | No description available
Lp | No description available
Lr | No description available
Pt | No description available
S2 | No description available
S6 | No description available
SA | No description available
SB | No description available
SC | No description available
SD | No description available
SE | No description available
SF | No description available
SG | No description available
SH | No description available
SI | No description available
SJ | No description available
SK | No description available
SL | No description available
SN | No description available
SO | No description available
SP | No description available
SQ | No description available
SR | No description available
SS | No description available
ST | No description available
SU | No description available
SV | No description available
SW | No description available
SX | No description available
SY | No description available
SZ | No description available
Sa | No description available
Sb | No description available
Sc | No description available
Sd | No description available
Se | No description available
Sg | No description available
mR | No description available
> select add #2
210694 atoms, 226602 bonds, 7666 pseudobonds, 16834 residues, 4 models
selected
> color (#!2 & sel) magenta
> show sel cartoons
> hide sel atoms
> select #1/mR, Sa
Nothing selected
> select #2/mR, Sa
1139 atoms, 1189 bonds, 23 pseudobonds, 122 residues, 2 models selected
> hide sel cartoons
> hide #!1 models
> undo
[Repeated 1 time(s)]
> select ~sel & ##selected
209555 atoms, 225413 bonds, 7643 pseudobonds, 16712 residues, 4 models
selected
> hide sel cartoons
> hide #!1 models
> select clear
> select #2/mR
305 atoms, 340 bonds, 15 residues, 1 model selected
> color sel hot pink
> select clear
> select #2/mR
305 atoms, 340 bonds, 15 residues, 1 model selected
> ui tool show "Color Actions"
> color sel pale violet red
> color sel plum
> select #2/mR
305 atoms, 340 bonds, 15 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 305 atom styles
> cartoon style nucleic xsection round width 1.6 thickness 0.7
> cartoon style nucleic xsection round width 1.6 thickness 0.5
[Repeated 1 time(s)]
> cartoon style nucleic xsection round width 1.3 thickness 0.5
> select clear
> select #2/mR, Sa
1139 atoms, 1189 bonds, 23 pseudobonds, 122 residues, 2 models selected
> view sel
> hide #2.1 models
> ui tool show "Surface Zone"
> surface zone #1 nearAtoms #2 distance 5.05
> show #!1 models
> surface zone #1 nearAtoms sel distance 5.05
> surface zone #1 nearAtoms sel distance 6.04
> volume #1 step 1
> volume #1 level 2.86
> volume #1 level 3.794
> close #1
> open
> /yonath_group/disha/RPS26/models_maps/Control_Kozak/new_tRNA_maps/maps/60s_40s_multibody_aligned2shiny_kozak_control_tRNA_with_blush_inverted_again.mrc
Opened
60s_40s_multibody_aligned2shiny_kozak_control_tRNA_with_blush_inverted_again.mrc
as #1, grid size 480,480,480, pixel 0.842, shown at level 0.00874, step 2,
values float32
> select #2/mR, Sa
1139 atoms, 1189 bonds, 23 pseudobonds, 122 residues, 2 models selected
> surface zone #1 nearAtoms sel distance 5.05
> volume #1 step 1
> volume #1 level 0.005
> surface zone #1 nearAtoms sel distance 3.35
> volume style mesh
> color #1 #dfdfdfff models
> color #1 #f1f1f1ff models
> show sel atoms
> style sel stick
Changed 1139 atom styles
> hide sel cartoons
> show sel cartoons
> color #1 #d6d6d6ff models
> color #1 #d4d4d4ff models
> color #1 #e6e6e6ff models
> color #1 #c8c8c8ff models
> color #1 #c7c7c7ff models
> color #1 #a6a6a6ff models
> lighting soft
> lighting full
> lighting shadows false
> select #2/mR
305 atoms, 340 bonds, 15 residues, 1 model selected
> color sel hot pink
> color sel byhetero
> select #2/mR, Sa
1139 atoms, 1189 bonds, 23 pseudobonds, 122 residues, 2 models selected
> surface zone #1 nearAtoms sel distance 2.63
> select add #2
210694 atoms, 226602 bonds, 7666 pseudobonds, 16834 residues, 4 models
selected
> show sel atoms
> undo
> select #2/mR, Sa
1139 atoms, 1189 bonds, 23 pseudobonds, 122 residues, 2 models selected
> view sel
> select clear
> volume style surface
> transparency #1#2.2-3#!2 60
> select clear
> open
> /yonath_group/disha/RPS26/models_maps/Control_Kozak/new_tRNA_maps/maps/60s_40s_FR_aligned2shiny_kozak_control_tRNA_with_blush_inverted_again_EMReady.mrc
Opened
60s_40s_FR_aligned2shiny_kozak_control_tRNA_with_blush_inverted_again_EMReady.mrc
as #3, grid size 480,480,480, pixel 0.842, shown at level 7.42, step 2, values
float32
> select add #3
4 models selected
> ui tool show "Color Actions"
> color sel pink
> transparency #3.1 70
> volume #3 step 4
> volume #3 level -0.07419
> volume #3 level 1.382
> view
> select clear
> hide #!1 models
> graphics silhouettes true
> select #2/mR, Sa
1139 atoms, 1189 bonds, 23 pseudobonds, 122 residues, 2 models selected
> show sel surfaces
> select clear
> select #2/mR
305 atoms, 340 bonds, 15 residues, 1 model selected
> color (#!2 & sel) red
> color (#!2 & sel) black
> select clear
> select #2/mR
305 atoms, 340 bonds, 15 residues, 1 model selected
> color (#!2 & sel) red
> select clear
> select #2/Pt
1653 atoms, 1843 bonds, 66 pseudobonds, 79 residues, 2 models selected
> color (#!2 & sel) lime
> show sel surfaces
> hide sel atoms
> select clear
> select #2/Sa
834 atoms, 849 bonds, 23 pseudobonds, 107 residues, 2 models selected
> ui tool show "Color Actions"
> color sel blue violet
> undo
> select clear
> select add #3
2 models selected
> transparency #3.1 80
> select clear
> select add #3
2 models selected
> select #2/mR
305 atoms, 340 bonds, 15 residues, 1 model selected
> color (#!2 & sel) orange red
> color (#!2 & sel) orange
> select clear
[Repeated 1 time(s)]
> ui tool show "Color Actions"
> color goldenrod
> undo
> select clear
> select #2/mR
305 atoms, 340 bonds, 15 residues, 1 model selected
> color sel goldenrod
[Repeated 1 time(s)]
> color sel dark orange
> color sel dark goldenrod
> color sel dark khaki
> color sel salmon
> color sel dark orange
> select #2/Sa
834 atoms, 849 bonds, 23 pseudobonds, 107 residues, 2 models selected
> color sel orchid
> color sel dark orchid
> color sel dark violet
> color sel blue violet
> select clear
> select add #3
2 models selected
> transparency #3.1 60
> select clear
> select add #3
2 models selected
> transparency #3.1 70
> select clear
> volume #3 step 2
> select clear
> close #3
> open
> /yonath_group/disha/RPS26/models_maps/Control_Kozak/new_tRNA_maps/maps/60s_40s_multibody_aligned2shiny_kozak_control_tRNA_with_blush_inverted_again.mrc
Opened
60s_40s_multibody_aligned2shiny_kozak_control_tRNA_with_blush_inverted_again.mrc
as #3, grid size 480,480,480, pixel 0.842, shown at level 0.00874, step 2,
values float32
> volume #3 level 0.005
> volume #3 step 1
> surface dust #3 size 8.42
> select add #3
2 models selected
> ui tool show "Color Actions"
> color sel pink
> transparency #3.1 80
> select clear
> volume #3 level 0.007
> volume #3 level 0.006
> volume #3 level 0.005
> select clear
> save /yonath_group/disha/Thesis_figures/rps26_kozak_control_whole_ribo.png
> width 1095 height 818 supersample 3
> save /yonath_group/disha/Thesis_figures/rps26_kozak_control_whole_ribo.cxs
\u2014\u2014\u2014 End of log from Wed Aug 28 16:36:21 2024 \u2014\u2014\u2014
opened ChimeraX session
> select #2/mR, Sa, Pt
2792 atoms, 3032 bonds, 96 pseudobonds, 201 residues, 2 models selected
> hide sel surfaces
> show sel cartoons
> show sel atoms
> style sel stick
Changed 2792 atom styles
> select add #3
2792 atoms, 3032 bonds, 96 pseudobonds, 201 residues, 7 models selected
> select subtract #3
2792 atoms, 3032 bonds, 96 pseudobonds, 201 residues, 5 models selected
> hide #!3 models
> show #!1 models
> ui tool show "Surface Zone"
> surface zone #1 nearAtoms sel distance 2.63
> select clear
> select #2/mR, Sa, Pt
2792 atoms, 3032 bonds, 96 pseudobonds, 201 residues, 2 models selected
> select #2/mR
305 atoms, 340 bonds, 15 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select #2/Sa
834 atoms, 849 bonds, 23 pseudobonds, 107 residues, 2 models selected
> color (#!2 & sel) magenta
> select clear
> save /yonath_group/disha/Thesis_figures/rps26_kozak_control_zoom_mRNA.cxs
> color zone #1 near #2 distance 5.05
> undo
> select #2/mR
305 atoms, 340 bonds, 15 residues, 1 model selected
> color (#!2 & sel) orange
> select clear
> color zone #1 near #2 distance 5.05
> transparency #1#2.2-6#!2 80
> select clear
> undo
[Repeated 2 time(s)]
> select clear
> save /yonath_group/disha/Thesis_figures/rps26_kozak_control_zoom_mRNA.cxs
> save /yonath_group/disha/Thesis_figures/rps26_kozak_control_zoom_mRNA.png
> width 1095 height 818 supersample 3
> hide #!1 models
> select clear
Drag select of 60 atoms, 12 residues, 58 bonds
> select clear
> select #2/Pt
1653 atoms, 1843 bonds, 66 pseudobonds, 79 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> select clear
> ui tool show Contacts
Drag select of 38 atoms, 4 residues, 41 bonds
> select clear
Drag select of 64 atoms, 12 residues, 61 bonds
> ui tool show Contacts
> contacts sel restrict both intraMol false ignoreHiddenModels true color
> #000000 dashes 8 radius 0.015 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
20 contacts
atom1 atom2 overlap distance
/Sa ALA 106 CB /mR G 27 P 0.180 3.800
/mR U 29 OP2 /Sa PRO 107 C 0.166 3.014
/mR G 27 OP1 /Sa GLY 105 CA 0.038 3.262
/mR C 26 P /Sa PRO 103 CA 0.029 3.951
/Sa ALA 106 CB /mR G 27 OP2 0.004 3.296
/mR C 28 OP1 /Sa ALA 106 CB -0.002 3.302
/Sa PRO 103 CA /mR C 26 OP1 -0.027 3.327
/Sa PHE 101 CB /mR G 27 OP2 -0.058 3.358
/Sa ALA 106 N /mR G 27 OP1 -0.089 2.749
/mR C 26 OP1 /Sa PHE 101 O -0.107 2.947
/Sa ALA 106 N /mR G 27 P -0.114 3.854
/mR C 26 O5' /Sa PRO 103 CA -0.147 3.487
/Sa PRO 107 O /mR U 29 OP2 -0.161 3.001
/mR C 26 C5' /Sa ALA 104 N -0.169 3.689
/mR G 27 OP2 /Sa PHE 101 CA -0.219 3.519
/Sa PHE 101 C /mR G 27 OP2 -0.281 3.311
/Sa ALA 106 CB /mR G 27 OP1 -0.304 3.604
/Sa PRO 103 CB /mR C 26 P -0.323 4.303
/Sa GLY 105 C /mR G 27 OP1 -0.338 3.368
/mR G 27 P /Sa ARG 102 O -0.380 3.900
20 contacts
> select clear
> undo
> ui tool show Contacts
> contacts sel restrict both intraMol false ignoreHiddenModels true color
> #000000 dashes 8 radius 0.015 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
20 contacts
atom1 atom2 overlap distance
/Sa ALA 106 CB /mR G 27 P 0.180 3.800
/mR U 29 OP2 /Sa PRO 107 C 0.166 3.014
/mR G 27 OP1 /Sa GLY 105 CA 0.038 3.262
/mR C 26 P /Sa PRO 103 CA 0.029 3.951
/Sa ALA 106 CB /mR G 27 OP2 0.004 3.296
/mR C 28 OP1 /Sa ALA 106 CB -0.002 3.302
/Sa PRO 103 CA /mR C 26 OP1 -0.027 3.327
/Sa PHE 101 CB /mR G 27 OP2 -0.058 3.358
/Sa ALA 106 N /mR G 27 OP1 -0.089 2.749
/mR C 26 OP1 /Sa PHE 101 O -0.107 2.947
/Sa ALA 106 N /mR G 27 P -0.114 3.854
/mR C 26 O5' /Sa PRO 103 CA -0.147 3.487
/Sa PRO 107 O /mR U 29 OP2 -0.161 3.001
/mR C 26 C5' /Sa ALA 104 N -0.169 3.689
/mR G 27 OP2 /Sa PHE 101 CA -0.219 3.519
/Sa PHE 101 C /mR G 27 OP2 -0.281 3.311
/Sa ALA 106 CB /mR G 27 OP1 -0.304 3.604
/Sa PRO 103 CB /mR C 26 P -0.323 4.303
/Sa GLY 105 C /mR G 27 OP1 -0.338 3.368
/mR G 27 P /Sa ARG 102 O -0.380 3.900
20 contacts
> select clear
> show #!1 models
> hide #!1 models
> select #2/Sa
834 atoms, 849 bonds, 23 pseudobonds, 107 residues, 2 models selected
> hide sel atoms
> select clear
Drag select of 2 atoms, 2 bonds
Drag select of 43 atoms, 11 residues, 47 bonds, 14 pseudobonds
> ui tool show Contacts
> contacts sel restrict both intraMol false ignoreHiddenModels true color
> #000000 dashes 8 radius 0.015 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
18 contacts
atom1 atom2 overlap distance
/Sa ALA 106 CB /mR G 27 P 0.180 3.800
/mR G 27 OP1 /Sa GLY 105 CA 0.038 3.262
/mR C 26 P /Sa PRO 103 CA 0.029 3.951
/Sa ALA 106 CB /mR G 27 OP2 0.004 3.296
/mR C 28 OP1 /Sa ALA 106 CB -0.002 3.302
/Sa PRO 103 CA /mR C 26 OP1 -0.027 3.327
/Sa PHE 101 CB /mR G 27 OP2 -0.058 3.358
/Sa ALA 106 N /mR G 27 OP1 -0.089 2.749
/mR C 26 OP1 /Sa PHE 101 O -0.107 2.947
/Sa ALA 106 N /mR G 27 P -0.114 3.854
/mR C 26 O5' /Sa PRO 103 CA -0.147 3.487
/mR C 26 C5' /Sa ALA 104 N -0.169 3.689
/mR G 27 OP2 /Sa PHE 101 CA -0.219 3.519
/Sa PHE 101 C /mR G 27 OP2 -0.281 3.311
/Sa ALA 106 CB /mR G 27 OP1 -0.304 3.604
/Sa PRO 103 CB /mR C 26 P -0.323 4.303
/Sa GLY 105 C /mR G 27 OP1 -0.338 3.368
/mR G 27 P /Sa ARG 102 O -0.380 3.900
18 contacts
Drag select of 53 atoms, 14 residues, 57 bonds, 18 pseudobonds
> ui tool show Contacts
> contacts sel restrict both intraMol false ignoreHiddenModels true color
> #000000 dashes 8 radius 0.015 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
20 contacts
atom1 atom2 overlap distance
/Sa ALA 106 CB /mR G 27 P 0.180 3.800
/mR U 29 OP2 /Sa PRO 107 C 0.166 3.014
/mR G 27 OP1 /Sa GLY 105 CA 0.038 3.262
/mR C 26 P /Sa PRO 103 CA 0.029 3.951
/Sa ALA 106 CB /mR G 27 OP2 0.004 3.296
/mR C 28 OP1 /Sa ALA 106 CB -0.002 3.302
/Sa PRO 103 CA /mR C 26 OP1 -0.027 3.327
/Sa PHE 101 CB /mR G 27 OP2 -0.058 3.358
/Sa ALA 106 N /mR G 27 OP1 -0.089 2.749
/mR C 26 OP1 /Sa PHE 101 O -0.107 2.947
/Sa ALA 106 N /mR G 27 P -0.114 3.854
/mR C 26 O5' /Sa PRO 103 CA -0.147 3.487
/Sa PRO 107 O /mR U 29 OP2 -0.161 3.001
/mR C 26 C5' /Sa ALA 104 N -0.169 3.689
/mR G 27 OP2 /Sa PHE 101 CA -0.219 3.519
/Sa PHE 101 C /mR G 27 OP2 -0.281 3.311
/Sa ALA 106 CB /mR G 27 OP1 -0.304 3.604
/Sa PRO 103 CB /mR C 26 P -0.323 4.303
/Sa GLY 105 C /mR G 27 OP1 -0.338 3.368
/mR G 27 P /Sa ARG 102 O -0.380 3.900
20 contacts
> select #2/mR
305 atoms, 340 bonds, 15 residues, 1 model selected
> color sel byhetero
> select clear
> select /Sa:107
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #2/mR
305 atoms, 340 bonds, 15 residues, 1 model selected
> ui tool show Contacts
> contacts sel restrict both distanceOnly 3.0 intraMol false
> ignoreHiddenModels true color #000000 dashes 8 radius 0.015 reveal true log
> true
Ignore distances between atoms separated by 4 bonds or less
Detect intra-residue distances: False
Detect intra-molecule distances: False
2 distances
atom1 atom2 distance
/mR G 27 OP1 /Sa ALA 106 N 2.749
/mR C 26 OP1 /Sa PHE 101 O 2.947
2 distances
> ui tool show Contacts
> contacts sel restrict both distanceOnly 3.5 intraMol false
> ignoreHiddenModels true color #000000 dashes 8 radius 0.015 reveal true log
> true
Ignore distances between atoms separated by 4 bonds or less
Detect intra-residue distances: False
Detect intra-molecule distances: False
16 distances
atom1 atom2 distance
/Sa ALA 106 N /mR G 27 OP1 2.749
/mR C 26 OP1 /Sa PHE 101 O 2.947
/Sa PRO 107 O /mR U 29 OP2 3.001
/mR U 29 OP2 /Sa PRO 107 C 3.014
/Sa ALA 104 N /mR C 26 O5' 3.180
/Sa GLY 105 CA /mR G 27 OP1 3.262
/Sa ALA 106 CB /mR G 27 OP2 3.296
/mR C 28 OP1 /Sa ALA 106 CB 3.302
/Sa PHE 101 O /mR G 27 OP2 3.310
/mR G 27 OP2 /Sa PHE 101 C 3.311
/Sa PRO 103 CA /mR C 26 OP1 3.327
/Sa PHE 101 CB /mR G 27 OP2 3.358
/mR G 27 OP1 /Sa GLY 105 N 3.366
/Sa GLY 105 C /mR G 27 OP1 3.368
/Sa ARG 102 O /mR G 27 OP2 3.375
/mR C 26 O5' /Sa PRO 103 CA 3.487
16 distances
> ui tool show Contacts
> contacts sel restrict both distanceOnly 3.2 intraMol false
> ignoreHiddenModels true color #000000 dashes 8 radius 0.015 reveal true log
> true
Ignore distances between atoms separated by 4 bonds or less
Detect intra-residue distances: False
Detect intra-molecule distances: False
5 distances
atom1 atom2 distance
/mR G 27 OP1 /Sa ALA 106 N 2.749
/mR C 26 OP1 /Sa PHE 101 O 2.947
/Sa PRO 107 O /mR U 29 OP2 3.001
/mR U 29 OP2 /Sa PRO 107 C 3.014
/mR C 26 O5' /Sa ALA 104 N 3.180
5 distances
> ui tool show Contacts
> contacts sel restrict both distanceOnly 3.3 intraMol false
> ignoreHiddenModels true color #000000 dashes 8 radius 0.015 reveal true log
> true
Ignore distances between atoms separated by 4 bonds or less
Detect intra-residue distances: False
Detect intra-molecule distances: False
7 distances
atom1 atom2 distance
/Sa ALA 106 N /mR G 27 OP1 2.749
/mR C 26 OP1 /Sa PHE 101 O 2.947
/Sa PRO 107 O /mR U 29 OP2 3.001
/mR U 29 OP2 /Sa PRO 107 C 3.014
/mR C 26 O5' /Sa ALA 104 N 3.180
/mR G 27 OP1 /Sa GLY 105 CA 3.262
/mR G 27 OP2 /Sa ALA 106 CB 3.296
7 distances
> ui tool show Contacts
> contacts sel restrict both intraMol false ignoreHiddenModels true color
> #000000 dashes 8 radius 0.015 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
20 contacts
atom1 atom2 overlap distance
/Sa ALA 106 CB /mR G 27 P 0.180 3.800
/mR U 29 OP2 /Sa PRO 107 C 0.166 3.014
/mR G 27 OP1 /Sa GLY 105 CA 0.038 3.262
/mR C 26 P /Sa PRO 103 CA 0.029 3.951
/Sa ALA 106 CB /mR G 27 OP2 0.004 3.296
/mR C 28 OP1 /Sa ALA 106 CB -0.002 3.302
/Sa PRO 103 CA /mR C 26 OP1 -0.027 3.327
/Sa PHE 101 CB /mR G 27 OP2 -0.058 3.358
/Sa ALA 106 N /mR G 27 OP1 -0.089 2.749
/mR C 26 OP1 /Sa PHE 101 O -0.107 2.947
/Sa ALA 106 N /mR G 27 P -0.114 3.854
/mR C 26 O5' /Sa PRO 103 CA -0.147 3.487
/Sa PRO 107 O /mR U 29 OP2 -0.161 3.001
/mR C 26 C5' /Sa ALA 104 N -0.169 3.689
/mR G 27 OP2 /Sa PHE 101 CA -0.219 3.519
/Sa PHE 101 C /mR G 27 OP2 -0.281 3.311
/Sa ALA 106 CB /mR G 27 OP1 -0.304 3.604
/Sa PRO 103 CB /mR C 26 P -0.323 4.303
/Sa GLY 105 C /mR G 27 OP1 -0.338 3.368
/mR G 27 P /Sa ARG 102 O -0.380 3.900
20 contacts
> select clear
> select #2/mR
305 atoms, 340 bonds, 15 residues, 1 model selected
> color sel byhetero
> select clear
> cartoon style nucleic xsection round width 1.3 thickness 0.3
> cartoon style nucleic xsection round width 1.0 thickness 0.5
> select clear
> save
> /yonath_group/disha/Thesis_figures/rps26_kozak_control_zoom_mRNA_interaction_ct.png
> width 1060 height 818 supersample 3
> select /Sa:107
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> save
> /yonath_group/disha/Thesis_figures/rps26_kozak_control_zoom_mRNA_interaction_ct.png
> width 1060 height 818 supersample 3
> save
> /yonath_group/disha/Thesis_figures/rps26_kozak_control_zoom_mRNA_interaction_ct.cxs
> select clear
Drag select of 41 atoms, 18 residues, 43 bonds
> ui tool show Contacts
> contacts sel restrict both intraMol false ignoreHiddenModels true color
> #000000 dashes 8 radius 0.015 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
8 contacts
atom1 atom2 overlap distance
/mR G 31 P /Sa SER 81 OG 0.409 3.151
/mR C 32 C5' /Sa HIS 80 CD2 0.076 3.564
/mR C 32 OP2 /Sa HIS 80 CD2 0.055 3.125
/Sa HIS 80 NE2 /mR C 32 C5' -0.082 3.602
/Sa SER 81 CA /mR C 32 OP2 -0.097 3.397
/mR G 31 O5' /Sa SER 81 OG -0.141 2.661
/mR C 32 P /Sa HIS 80 CD2 -0.141 4.001
/mR G 31 OP1 /Sa SER 81 O -0.239 3.079
8 contacts
> select clear
> select /Sa:81
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select /Sa:82
9 atoms, 8 bonds, 1 residue, 1 model selected
Drag select of 48 atoms, 12 residues, 53 bonds, 8 pseudobonds
> ui tool show Contacts
> contacts sel restrict both intraMol false ignoreHiddenModels true color
> #000000 dashes 8 radius 0.015 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
8 contacts
atom1 atom2 overlap distance
/mR G 31 P /Sa SER 81 OG 0.409 3.151
/mR C 32 C5' /Sa HIS 80 CD2 0.076 3.564
/mR C 32 OP2 /Sa HIS 80 CD2 0.055 3.125
/Sa HIS 80 NE2 /mR C 32 C5' -0.082 3.602
/Sa SER 81 CA /mR C 32 OP2 -0.097 3.397
/mR G 31 O5' /Sa SER 81 OG -0.141 2.661
/mR C 32 P /Sa HIS 80 CD2 -0.141 4.001
/mR G 31 OP1 /Sa SER 81 O -0.239 3.079
8 contacts
> select clear
> select /Sa:83
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /Sa:82
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> undo
[Repeated 1 time(s)]
> hide sel atoms
> select clear
[Repeated 1 time(s)]
> save
> /yonath_group/disha/Thesis_figures/rps26_kozak_control_zoom_mRNA_interaction_his.cxs
> save
> /yonath_group/disha/Thesis_figures/rps26_kozak_control_zoom_mRNA_interaction_his.png
> width 1060 height 818 supersample 3
> close session
> open
> /yonath_group/disha/RPS26/models_maps/Control_TISU/new_model_maps/RPS26_control_TISU_tRNA/maps/multibody_60s_40s_rps26_control_tisu_tRNA_aligned2shiny.mrc
Opened multibody_60s_40s_rps26_control_tisu_tRNA_aligned2shiny.mrc as #1, grid
size 480,480,480, pixel 0.842, shown at level 0.0064, step 2, values float32
> volume #1 level 0.005
> volume #1 step 1
> open
> /yonath_group/disha/RPS26/models_maps/Control_TISU/new_model_maps/RPS26_control_TISU_tRNA/models/Phenix/RealSpaceRefine_9/RPS26_control_TISU_real_space_refined_009-coot-0.cif
Summary of feedback from opening
/yonath_group/disha/RPS26/models_maps/Control_TISU/new_model_maps/RPS26_control_TISU_tRNA/models/Phenix/RealSpaceRefine_9/RPS26_control_TISU_real_space_refined_009-coot-0.cif
---
warnings | Skipping chem_comp category: Missing column 'type' near line 190
Missing entity information. Treating each chain as a separate entity.
Unknown polymer entity '1' near line 206217
Atom . is not in the residue template for LYS /SP:145
Missing or incomplete sequence information. Inferred polymer connectivity.
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 334, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 131, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 294, in provider_open
session.models.add(opened_models)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/models.py", line 757, in add
m.added_to_session(session)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1280, in added_to_session
self._report_chain_descriptions(session)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1546, in
_report_chain_descriptions
self._report_chain_summary(session, descripts, chain_text, False)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1696, in _report_chain_summary
uids = uniprot_ids(self)
^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 2591, in uniprot_ids
uids = uniprot_ids(structure)
^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/mmcif/uniprot_id.py", line 36, in uniprot_ids
db_refs = database_ref.mapping('id', ['db_name', 'db_code',
'pdbx_db_accession'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "src/mmcif.pyx", line 1002, in chimerax.mmcif.mmcif.CIFTable.mapping
chimerax.mmcif.mmcif.TableMissingFieldsError: Field "id" not in table
"struct_ref", have fields "db_name" and "db_code"
chimerax.mmcif.mmcif.TableMissingFieldsError: Field "id" not in table
"struct_ref", have fields "db_name" and "db_code"
File "src/mmcif.pyx", line 1002, in chimerax.mmcif.mmcif.CIFTable.mapping
See log for complete Python traceback.
> close session
> open
> /yonath_group/disha/RPS26/models_maps/Control_TISU/new_model_maps/RPS26_control_TISU_tRNA/maps/multibody_60s_40s_rps26_control_tisu_tRNA_aligned2shiny.mrc
> format mrc
Opened multibody_60s_40s_rps26_control_tisu_tRNA_aligned2shiny.mrc as #1, grid
size 480,480,480, pixel 0.842, shown at level 0.0064, step 2, values float32
> open
> /yonath_group/disha/RPS26/models_maps/Control_TISU/new_model_maps/RPS26_control_TISU_tRNA/models/Phenix/RealSpaceRefine_9/RPS26_control_TISU_real_space_refined_009-coot-1.cif
Summary of feedback from opening
/yonath_group/disha/RPS26/models_maps/Control_TISU/new_model_maps/RPS26_control_TISU_tRNA/models/Phenix/RealSpaceRefine_9/RPS26_control_TISU_real_space_refined_009-coot-1.cif
---
warnings | Skipping chem_comp category: Missing column 'type' near line 19
Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for RPS26_control_TISU_real_space_refined_009-coot-1.cif #2
---
Chain | Description
L5 | No description available
L7 | No description available
L8 | No description available
LA | No description available
LB | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
LQ | No description available
LR | No description available
LS | No description available
LT | No description available
LU | No description available
LV | No description available
LW | No description available
LX | No description available
LY | No description available
LZ | No description available
La | No description available
Lb | No description available
Lc | No description available
Ld | No description available
Le | No description available
Lf | No description available
Lg | No description available
Lh | No description available
Li | No description available
Lj | No description available
Lk | No description available
Ll | No description available
Lm | No description available
Ln | No description available
Lo | No description available
Lp | No description available
Lr | No description available
Pt | No description available
S2 | No description available
SA | No description available
SB | No description available
SC | No description available
SD | No description available
SE | No description available
SF | No description available
SG | No description available
SH | No description available
SI | No description available
SJ | No description available
SK | No description available
SL | No description available
SN | No description available
SO | No description available
SP | No description available
SQ | No description available
SR | No description available
SS | No description available
ST | No description available
SU | No description available
SV | No description available
SW | No description available
SX | No description available
SY | No description available
SZ | No description available
Sa | No description available
Sb | No description available
Sc | No description available
Sd | No description available
Se | No description available
Sf | No description available
Sg | No description available
mR | No description available
> volume #1 step 1
> volume #1 level 0.005
> select clear
> select add #2
209197 atoms, 224879 bonds, 32 pseudobonds, 16782 residues, 2 models selected
> ui tool show "Color Actions"
> color sel blue violet
> color sel magenta
> show sel cartoons
> hide sel atoms
> select clear
> open
> /yonath_group/disha/RPS26/models_maps/Control_TISU/new_model_maps/RPS26_control_TISU_tRNA/maps/multibody_60s_40s_rps26_control_tisu_tRNA_aligned2shiny.mrc
Opened multibody_60s_40s_rps26_control_tisu_tRNA_aligned2shiny.mrc as #3, grid
size 480,480,480, pixel 0.842, shown at level 0.0064, step 2, values float32
> select add #3
2 models selected
> ui tool show "Color Actions"
> color sel pink
> hide #!1 models
> volume #3 level 0.004
> volume #3 level 0.005
> volume #3 step 1
> surface dust #3 size 8.42
> hide #!2 models
> volume #3 step 2
> volume #3 step 4
> volume #3 step 1
> volume #3 level 0.004
> select clear
> select add #3
2 models selected
> transparency #3.1 70
> select clear
> select #2/mR, Sa, Pt
2592 atoms, 2813 bonds, 185 residues, 1 model selected
> show #!2 models
> select ~sel & ##selected
206605 atoms, 222066 bonds, 32 pseudobonds, 16597 residues, 2 models selected
> hide sel cartoons
> select #2/mR, Sa, Pt
2592 atoms, 2813 bonds, 185 residues, 1 model selected
> select clear
> select #2/mR
152 atoms, 170 bonds, 7 residues, 1 model selected
> color sel orange
> show sel atoms
> select #2/Pt
1654 atoms, 1844 bonds, 79 residues, 1 model selected
> color sel lime
> select #2/mR, Sa, Pt
2592 atoms, 2813 bonds, 185 residues, 1 model selected
> show sel surfaces
> select clear
[Repeated 1 time(s)]
> select #2/Sa
786 atoms, 799 bonds, 99 residues, 1 model selected
> ui tool show "Color Actions"
> color sel blue violet
> select clear
> save /yonath_group/disha/Thesis_figures/rps26_TISU_control_whole_ribo.png
> width 1060 height 818 supersample 3
> save /yonath_group/disha/Thesis_figures/rps26_TISU_control_whole_ribo.cxs
> hide surfaces
> hide #!3 models
> select #2/mR, Sa, Pt
2592 atoms, 2813 bonds, 185 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 2592 atom styles
> select clear
> show #!1 models
> select #2/mR, Sa, Pt
2592 atoms, 2813 bonds, 185 residues, 1 model selected
> ui tool show "Surface Zone"
> surface zone #1 nearAtoms sel distance 5.05
> surface zone #1 nearAtoms sel distance 2.49
> surface zone #1 nearAtoms sel distance 3.09
> view sel
> transparency (#!2 & sel) 50
> select clear
> transparency #1-2 50
> cartoon style nucleic xsection round width 1.3 thickness 0.3
> select #2/Sa
786 atoms, 799 bonds, 99 residues, 1 model selected
> color (#!2 & sel) magenta
> select clear
> select #2/mR, Sa, Pt
2592 atoms, 2813 bonds, 185 residues, 1 model selected
> surface zone #1 nearAtoms sel distance 3.17
> volume #1 level 0.004
> surface dust #1 size 8.42
> surface zone #1 nearAtoms sel distance 3.17
> surface zone #1 nearAtoms sel distance 4.76
> surface zone #1 nearAtoms sel distance 3.37
> select clear
> select #2/mR, Sa, Pt
2592 atoms, 2813 bonds, 185 residues, 1 model selected
> surface zone #1 nearAtoms sel distance 2.15
> select clear
> save /yonath_group/disha/Thesis_figures/rps26_TISU_control_zoom_mRNA.cxs
\u2014\u2014\u2014 End of log from Wed Aug 28 17:08:09 2024 \u2014\u2014\u2014
opened ChimeraX session
> hide #!1 models
> select #2/mR, Sa, Pt
2592 atoms, 2813 bonds, 185 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #2/S2
32952 atoms, 36835 bonds, 10 pseudobonds, 1541 residues, 2 models selected
> show sel cartoons
> ui tool show "Color Actions"
> color sel light pink
> select #2/S2:1207
23 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 23 atom styles
> select clear
Drag select of 31 residues
Drag select of 814 residues, 7 pseudobonds
> select clear
Drag select of 806 residues, 7 pseudobonds
> hide sel cartoons
Drag select of 58 residues
> hide sel cartoons
> view
Drag select of 151 residues
> hide sel cartoons
Drag select of 188 residues, 1 pseudobonds
> hide sel cartoons
Drag select of 50 residues
> hide sel cartoons
Drag select of 9 residues
> hide sel cartoons
Drag select of 38 residues, 1 pseudobonds
> hide sel cartoons
Drag select of 26 residues
> hide sel cartoons
Drag select of 61 residues
> hide sel cartoons
Drag select of 3 residues
> hide sel cartoons
Drag select of 13 residues
> hide sel cartoons
> select #2/mR, Sa, Pt
2592 atoms, 2813 bonds, 185 residues, 1 model selected
> show sel cartoons
> show sel atoms
> cartoon style nucleic xsection round width 1.0 thickness 0.5
> select #2/S2:1207
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #2/S2
32952 atoms, 36835 bonds, 10 pseudobonds, 1541 residues, 2 models selected
> show sel surfaces
> transparency (#!2 & sel) 80
> select clear
> select #2/Sa
786 atoms, 799 bonds, 99 residues, 1 model selected
> hide sel atoms
> select clear
> save /yonath_group/disha/Thesis_figures/rps26_TISU_control_1207_whole.cxs
> save /yonath_group/disha/Thesis_figures/rps26_TISU_control_1207_whole.png
> width 978 height 818 supersample 3
> hide surfaces
> select #2/mR
152 atoms, 170 bonds, 7 residues, 1 model selected
> color sel byhetero
> select clear
> select /S2:1207
23 atoms, 25 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
Drag select of 13 atoms, 4 residues, 16 bonds
Drag select of 18 atoms, 15 residues, 22 bonds
> ui tool show Contacts
> contacts sel restrict both intraMol false ignoreHiddenModels true color
> #000000 dashes 8 radius 0.015 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
8 contacts
atom1 atom2 overlap distance
/S2 U 1046 OP1 /S2 U 946 C4' 0.039 3.261
/S2 G 1065 C5' /S2 U 960 C5' -0.127 3.887
/S2 G 1065 C4' /S2 G 959 O2' -0.186 3.526
/S2 U 1046 C5' /S2 U 945 O2' -0.208 3.548
/S2 U 1046 P /S2 U 946 C4' -0.243 4.223
/S2 U 946 C1' /S2 U 1045 O2' -0.340 3.680
/S2 U 1045 O3' /S2 U 946 C1' -0.361 3.701
/S2 U 1045 O2' /S2 U 945 O2 -0.393 2.873
8 contacts
> undo
> select clear
Drag select of 71 atoms, 31 residues, 8 pseudobonds
> hide sel atoms
> select /mR:33
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
Drag select of 11 atoms, 13 bonds
> ui tool show Contacts
> contacts sel restrict both intraMol false ignoreHiddenModels true color
> #000000 dashes 8 radius 0.015 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
0 contacts
atom1 atom2 overlap distance
No contacts
> select clear
Drag select of 20 atoms, 6 residues, 22 bonds
> select clear
Drag select of 18 atoms, 11 residues, 20 bonds
> select /S2:1063
20 atoms, 21 bonds, 1 residue, 1 model selected
> undo
[Repeated 1 time(s)]
> select clear
> undo
> select clear
Drag select of 16 atoms, 8 residues, 19 bonds
Drag select of 14 atoms, 2 residues, 15 bonds
Drag select of 12 atoms, 4 residues, 14 bonds
> select clear
Drag select of 2 residues
> hide sel cartoons
Drag select of 18 atoms, 3 residues, 24 bonds
> ui tool show Contacts
> contacts sel restrict both distanceOnly 4.5 intraMol false
> ignoreHiddenModels true color #000000 dashes 8 radius 0.015 reveal true log
> true
Ignore distances between atoms separated by 4 bonds or less
Detect intra-residue distances: False
Detect intra-molecule distances: False
37 distances
atom1 atom2 distance
/S2 G 1207 N1 /mR A 37 OP2 2.719
/S2 G 1207 N2 /mR A 37 OP1 3.238
/S2 G 1207 O6 /mR A 37 OP2 3.450
/S2 G 1207 N2 /mR A 37 OP2 3.503
/mR A 37 OP2 /S2 G 1207 C6 3.539
/S2 G 1207 C2 /mR A 37 OP2 3.596
/S2 G 1207 N2 /mR A 37 P 3.745
/S2 G 1207 N3 /mR G 36 N1 3.766
/S2 G 1207 N2 /mR G 36 C5 3.776
/mR A 37 P /S2 G 1207 N1 3.812
/S2 G 1207 N2 /mR G 36 C4 3.815
/S2 G 1207 N3 /mR G 36 C6 3.923
/mR G 36 C3' /S2 G 1207 N2 3.933
/mR A 37 OP1 /S2 G 1207 N1 4.034
/mR G 36 N7 /S2 G 1207 N2 4.051
/S2 G 1207 N3 /mR G 36 C2 4.062
/mR G 36 N9 /S2 G 1207 N2 4.095
/S2 G 1207 C2 /mR A 37 OP1 4.126
/S2 G 1207 N2 /mR G 36 C6 4.163
/mR G 36 C8 /S2 G 1207 N2 4.197
/mR G 36 C4 /S2 G 1207 C2 4.241
/S2 G 1207 N2 /mR G 36 N3 4.243
/mR G 36 C2 /S2 G 1207 C2 4.244
/S2 G 1207 C2 /mR G 36 N1 4.267
/mR G 36 N3 /S2 G 1207 C2 4.272
/S2 G 1207 C4 /mR G 36 N1 4.280
/mR G 36 O6 /S2 G 1207 N3 4.285
/mR G 36 C5 /S2 G 1207 C2 4.299
/S2 G 1207 N3 /mR G 36 C5 4.313
/S2 G 1207 C2 /mR A 37 P 4.314
/mR G 36 C2' /S2 G 1207 N2 4.324
/mR G 36 O3' /S2 G 1207 N2 4.330
/mR G 36 C6 /S2 G 1207 C2 4.339
/S2 G 1207 C4 /mR G 36 C2 4.432
/mR G 36 N1 /S2 G 1207 C1' 4.451
/S2 G 1207 N2 /mR G 36 N1 4.467
/S2 G 1207 N3 /mR G 36 N3 4.483
37 distances
> ui tool show Contacts
> contacts sel restrict both intraMol false ignoreHiddenModels true color
> #000000 dashes 8 radius 0.015 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
3 contacts
atom1 atom2 overlap distance
/S2 G 1207 N2 /mR A 37 P -0.005 3.745
/mR A 37 OP2 /S2 G 1207 N1 -0.059 2.719
/mR A 37 P /S2 G 1207 N1 -0.072 3.812
3 contacts
> hide #3.1 models
> hide #2.6 models
> select clear
Drag select of 2 residues
> hide sel cartoons
Drag select of 41 residues
> select clear
Drag select of 53 residues
> hide sel cartoons
Drag select of 7 residues
> hide sel cartoons
Drag select of 1 residues
> hide sel cartoons
> select clear
Drag select of 2 residues
> hide sel cartoons
Drag select of 9 residues
> hide sel cartoons
Drag select of 3 residues
> hide sel cartoons
Drag select of 1 atoms
> hide sel atoms
> save /yonath_group/disha/Thesis_figures/rps26_TISU_control_1207_zoom.png
> width 978 height 818 supersample 3
> save /yonath_group/disha/Thesis_figures/rps26_TISU_control_1207_zoom.cxs
\u2014\u2014\u2014 End of log from Thu Aug 29 17:07:16 2024 \u2014\u2014\u2014
opened ChimeraX session
> select #2/mR
152 atoms, 170 bonds, 7 residues, 1 model selected
> ui tool show "Color Actions"
> color sel indian red
> color sel byhetero
> select clear
> select #2/S2
32952 atoms, 36835 bonds, 10 pseudobonds, 1541 residues, 2 models selected
> ui tool show "Color Actions"
> color sel tan
> color sel misty rose
> color sel pink
> color sel peru
> color sel dark salmon
> color sel salmon
> color sel coral
> color sel peach puff
> color sel moccasin
> color sel wheat
> color sel tan
> color sel rosy brown
> color sel light pink
> color sel thistle
[Repeated 1 time(s)]
> select #2/mR
152 atoms, 170 bonds, 7 residues, 1 model selected
> nucleotides sel fill
> style nucleic & sel stick
Changed 152 atom styles
> select clear
> select #2/pT
Nothing selected
> select #2/Pt
1654 atoms, 1844 bonds, 79 residues, 1 model selected
> nucleotides sel fill
> style nucleic & sel stick
Changed 1645 atom styles
> select clear
> undo
[Repeated 1 time(s)]
> nucleotides sel atoms
> style nucleic & sel stick
Changed 1645 atom styles
> select clear
> cartoon style nucleic xsection round width 1.0 thickness 0.3
[Repeated 1 time(s)]An error occurred in drawing the scene. Redrawing graphics
is now stopped to avoid a continuous stream of error messages. To restart
graphics use the command "graphics restart" after changing the settings that
caused the error.
GLError(
err = 1282,
description = b'invalid operation',
baseOperation = glDrawBuffer,
cArguments = (GL_BACK,)
)
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 84, in draw_new_frame
view.draw(check_for_changes = False)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 188, in draw
self._draw_scene(camera, drawings)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 270, in _draw_scene
silhouette.finish_silhouette_drawing(r)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1825, in finish_silhouette_drawing
fb = r.pop_framebuffer()
^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 764, in pop_framebuffer
fb.activate()
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 2313, in activate
GL.glDrawBuffer(self._draw_buffer)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1282,
description = b'invalid operation',
baseOperation = glDrawBuffer,
cArguments = (GL_BACK,)
)
OpenGL version: 3.3.0 NVIDIA 550.90.07
OpenGL renderer: Quadro RTX 4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=plasmax11
XDG_SESSION_DESKTOP=plasmax11
XDG_CURRENT_DESKTOP=KDE
DISPLAY=:1
Manufacturer: ASUS
Model: System Product Name
OS: Rocky Linux 9.4 Blue Onyx
Architecture: 64bit ELF
Virtual Machine: none
CPU: 24 AMD Ryzen 9 5900X 12-Core Processor
Cache Size: 512 KB
Memory:
total used free shared buff/cache available
Mem: 62Gi 35Gi 18Gi 959Mi 9.7Gi 26Gi
Swap: 31Gi 7.1Gi 24Gi
Graphics:
05:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU104GL [Quadro RTX 4000] [10de:1eb1] (rev a1)
Subsystem: NVIDIA Corporation Device [10de:12a0]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.22.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
distro: 1.7.0
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 23.2
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 12 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Graphics |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → cartoon style nucleic: glDrawBuffer: invalid operation |
comment:2 by , 12 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
We've seen this OpenGL error before, only on Linux. It seems to happen at random. Did your machine sleep and then wake up and give this error? Or was it using a remote X11 connection? The error says it cannot draw to the back buffer which suggests an issue related to the connection to the display.
GLError( err = 1282, description = b'invalid operation', baseOperation = glDrawBuffer, cArguments = (GL_BACK,) )
Note:
See TracTickets
for help on using tickets.
Reported by Disha Hiregange