id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16205 cartoon style nucleic: glDrawBuffer: invalid operation disha-gajanan.hiregange@… Tom Goddard "{{{ 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 }}} " defect closed normal Graphics can't reproduce Greg Couch all ChimeraX