id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20314 """cartoon suppress true"" displays cartoon" daniel.larsson@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-13.7.8-arm64-arm-64bit ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC) Description Load an RNA molecule. Hide all atoms and cartoons. Then show atoms and cartoon for part of the RNA molecule. Then run the command ""cartoon suppress true"". This will show cartoon for the full molecule. Log: UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. > open /Users/dalar193/wd/deltaRibosomes/EMDB_previews.cxs format session Opened 8emm_map as #1.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.01, step 1, values float32 Opened 8b0x_map as #1.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.23, step 1, values float32 Opened 8cgk_map as #1.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0065, step 1, values float32 Opened 7bv8_map as #1.8, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.11, step 1, values float32 Opened 7o1a_map as #1.10, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.025, step 1, values float32 Opened 8cam_map as #1.13, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.01, step 1, values float32 Opened 5mdz_emd_3493.map as #1.15, grid size 400,400,400, pixel 1.04, shown at level 0.1, step 1, values float32 Opened d9_ape as #2.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.01, step 1, values float32 Opened d9_ape1 as #2.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.01, step 1, values float32 Opened d9_ape2 as #2.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.01, step 1, values float32 Opened d9_ape3 as #2.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.01, step 1, values float32 Opened d9_pe as #2.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.01, step 1, values float32 Opened d9_e as #2.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.01, step 1, values float32 Opened d9_j169_conc as #2.7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.01, step 1, values float32 Opened d9_ape as #3.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0963, step 1, values float32 Opened d9_ape1 as #3.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0936, step 1, values float32 Opened d9_ape2 as #3.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0768, step 1, values float32 Opened d9_ape3 as #3.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0872, step 1, values float32 Opened d9_pe as #3.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0944, step 1, values float32 Opened d9_e as #3.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0736, step 1, values float32 Opened d9_J83_cl0 as #4.10, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.38, step 1, values float32 Opened d9_J84_cl1 as #4.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.38, step 1, values float32 Opened d9_J85_cl2 as #4.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.38, step 1, values float32 Opened d9_J86_cl3 as #4.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.38, step 1, values float32 Opened d9_J87_cl4 as #4.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.38, step 1, values float32 Opened d9_J88_cl5 as #4.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.38, step 1, values float32 Opened d9_J89_cl6 as #4.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.38, step 1, values float32 Opened d9_J90_cl7 as #4.7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.38, step 1, values float32 Opened d9_J91_cl8 as #4.8, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.38, step 1, values float32 Opened d9_J92_cl9 as #4.9, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.38, step 1, values float32 Opened d9_J83_cl0 as #5.10, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.33, step 1, values float32 Opened d9_J84_cl1 as #5.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.42, step 1, values float32 Opened d9_J85_cl2 as #5.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.38, step 1, values float32 Opened d9_J86_cl3 as #5.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.39, step 1, values float32 Opened d9_J87_cl4 as #5.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.38, step 1, values float32 Opened d9_J88_cl5 as #5.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.35, step 1, values float32 Opened d9_J89_cl6 as #5.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.38, step 1, values float32 Opened d9_J90_cl7 as #5.7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.39, step 1, values float32 Opened d9_J91_cl8 as #5.8, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.41, step 1, values float32 Opened d9_J92_cl9 as #5.9, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.37, step 1, values float32 Opened d10_ape as #10.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.009, step 1, values float32 Opened d10_pe as #10.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.009, step 1, values float32 Opened d10_e as #10.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.009, step 1, values float32 Opened d10_j064_conc as #10.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.009, step 1, values float32 Opened d10_ape as #11.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0779, step 1, values float32 Opened d10_pe as #11.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0807, step 1, values float32 Opened d10_e as #11.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0701, step 1, values float32 Opened d10_J53_c0 as #12.10, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J54_c1 as #12.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J55_c2 as #12.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J56_c3 as #12.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J57_c4 as #12.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J58_c5 as #12.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J59_c6 as #12.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J60_c7 as #12.7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J61_c8 as #12.8, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J62_c9 as #12.9, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J53_c0 as #13.10, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.19, step 1, values float32 Opened d10_J54_c1 as #13.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.21, step 1, values float32 Opened d10_J55_c2 as #13.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.2, step 1, values float32 Opened d10_J56_c3 as #13.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.23, step 1, values float32 Opened d10_J57_c4 as #13.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.2, step 1, values float32 Opened d10_J58_c5 as #13.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.21, step 1, values float32 Opened d10_J59_c6 as #13.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.23, step 1, values float32 Opened d10_J60_c7 as #13.7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.24, step 1, values float32 Opened d10_J61_c8 as #13.8, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.21, step 1, values float32 Opened d10_J62_c9 as #13.9, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.23, step 1, values float32 Opened dE_J230_ape as #20.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.056, step 1, values float32 Opened dE_J231_ap as #20.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.056, step 1, values float32 Opened dE_J232_pe as #20.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.056, step 1, values float32 Opened dE_J233_e as #20.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.056, step 1, values float32 Opened dE_J228_conc as #20.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.056, step 1, values float32 Opened dE_J111_ape as #21.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.25, step 1, values float32 Opened dE_J112_ap as #21.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.25, step 1, values float32 Opened dE_J113_pe as #21.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.25, step 1, values float32 Opened dE_J124_e as #21.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.25, step 1, values float32 Opened dE_J239_c0 as #23.10, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.07, step 1, values float32 Opened dE_J240_c1 as #23.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.07, step 1, values float32 Opened dE_J241_c2 as #23.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.07, step 1, values float32 Opened dE_J242_c3 as #23.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.065, step 1, values float32 Opened dE_J243_c4 as #23.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.07, step 1, values float32 Opened dE_J244_c5 as #23.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.07, step 1, values float32 Opened dE_J245_c6 as #23.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.07, step 1, values float32 Opened dE_J246_c7 as #23.7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.07, step 1, values float32 Opened dE_J247_c8 as #23.8, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.07, step 1, values float32 Opened dE_J248_c9 as #23.9, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.07, step 1, values float32 Log from Mon Oct 20 14:51:37 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/dalar193/wd/deltaRibosomes/EMDB_previews.cxs Opened 8emm_map as #1.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.01, step 1, values float32 Opened 8b0x_map as #1.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.23, step 1, values float32 Opened 8cgk_map as #1.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0065, step 1, values float32 Opened 7bv8_map as #1.8, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.11, step 1, values float32 Opened 7o1a_map as #1.10, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.025, step 1, values float32 Opened 8cam_map as #1.13, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.01, step 1, values float32 Opened 5mdz_emd_3493.map as #1.15, grid size 400,400,400, pixel 1.04, shown at level 0.1, step 1, values float32 Opened d9_ape as #2.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.012, step 1, values float32 Opened d9_ape1 as #2.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.012, step 1, values float32 Opened d9_ape2 as #2.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.012, step 1, values float32 Opened d9_ape3 as #2.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.012, step 1, values float32 Opened d9_pe as #2.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.012, step 1, values float32 Opened d9_e as #2.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.012, step 1, values float32 Opened d9_ape as #3.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0963, step 1, values float32 Opened d9_ape1 as #3.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0936, step 1, values float32 Opened d9_ape2 as #3.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0768, step 1, values float32 Opened d9_ape3 as #3.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0872, step 1, values float32 Opened d9_pe as #3.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0944, step 1, values float32 Opened d9_e as #3.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0736, step 1, values float32 Opened d9_J83_cl0 as #4.10, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.38, step 1, values float32 Opened d9_J84_cl1 as #4.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.38, step 1, values float32 Opened d9_J85_cl2 as #4.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.38, step 1, values float32 Opened d9_J86_cl3 as #4.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.38, step 1, values float32 Opened d9_J87_cl4 as #4.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.38, step 1, values float32 Opened d9_J88_cl5 as #4.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.38, step 1, values float32 Opened d9_J89_cl6 as #4.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.38, step 1, values float32 Opened d9_J90_cl7 as #4.7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.38, step 1, values float32 Opened d9_J91_cl8 as #4.8, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.38, step 1, values float32 Opened d9_J92_cl9 as #4.9, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.38, step 1, values float32 Opened d9_J83_cl0 as #5.10, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.33, step 1, values float32 Opened d9_J84_cl1 as #5.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.42, step 1, values float32 Opened d9_J85_cl2 as #5.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.38, step 1, values float32 Opened d9_J86_cl3 as #5.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.39, step 1, values float32 Opened d9_J87_cl4 as #5.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.38, step 1, values float32 Opened d9_J88_cl5 as #5.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.35, step 1, values float32 Opened d9_J89_cl6 as #5.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.38, step 1, values float32 Opened d9_J90_cl7 as #5.7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.39, step 1, values float32 Opened d9_J91_cl8 as #5.8, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.41, step 1, values float32 Opened d9_J92_cl9 as #5.9, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.37, step 1, values float32 Opened d10_ape as #10.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.011, step 1, values float32 Opened d10_pe as #10.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.011, step 1, values float32 Opened d10_e as #10.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.011, step 1, values float32 Opened d10_ape as #11.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0779, step 1, values float32 Opened d10_pe as #11.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0807, step 1, values float32 Opened d10_e as #11.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0701, step 1, values float32 Opened d10_J53_c0 as #12.10, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J54_c1 as #12.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J55_c2 as #12.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J56_c3 as #12.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J57_c4 as #12.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J58_c5 as #12.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J59_c6 as #12.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J60_c7 as #12.7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J61_c8 as #12.8, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J62_c9 as #12.9, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J53_c0 as #13.10, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.19, step 1, values float32 Opened d10_J54_c1 as #13.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.21, step 1, values float32 Opened d10_J55_c2 as #13.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.2, step 1, values float32 Opened d10_J56_c3 as #13.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.23, step 1, values float32 Opened d10_J57_c4 as #13.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.2, step 1, values float32 Opened d10_J58_c5 as #13.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.21, step 1, values float32 Opened d10_J59_c6 as #13.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.23, step 1, values float32 Opened d10_J60_c7 as #13.7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.24, step 1, values float32 Opened d10_J61_c8 as #13.8, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.21, step 1, values float32 Opened d10_J62_c9 as #13.9, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.23, step 1, values float32 Opened dE_J230_ape as #20.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.056, step 1, values float32 Opened dE_J231_ap as #20.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.056, step 1, values float32 Opened dE_J232_pe as #20.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.056, step 1, values float32 Opened dE_J233_e as #20.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.056, step 1, values float32 Opened dE_J228_conc as #20.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.056, step 1, values float32 Opened dE_J111_ape as #21.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.25, step 1, values float32 Opened dE_J112_ap as #21.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.25, step 1, values float32 Opened dE_J113_pe as #21.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.25, step 1, values float32 Opened dE_J124_e as #21.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.25, step 1, values float32 Opened dE_J239_c0 as #23.10, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.07, step 1, values float32 Opened dE_J240_c1 as #23.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.07, step 1, values float32 Opened dE_J241_c2 as #23.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.07, step 1, values float32 Opened dE_J242_c3 as #23.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.065, step 1, values float32 Opened dE_J243_c4 as #23.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.07, step 1, values float32 Opened dE_J244_c5 as #23.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.07, step 1, values float32 Opened dE_J245_c6 as #23.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.07, step 1, values float32 Opened dE_J246_c7 as #23.7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.07, step 1, values float32 Opened dE_J247_c8 as #23.8, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.07, step 1, values float32 Opened dE_J248_c9 as #23.9, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.07, step 1, values float32 Log from Sun Oct 12 20:03:57 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open EMDB_previews.cxs Opened 8emm_map as #1.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.01, step 1, values float32 Opened 8b0x_map as #1.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.23, step 1, values float32 Opened 8cgk_map as #1.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0065, step 1, values float32 Opened 7bv8_map as #1.8, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.11, step 1, values float32 Opened 7o1a_map as #1.10, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.025, step 1, values float32 Opened 8cam_map as #1.13, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.01, step 1, values float32 Opened 5mdz_emd_3493.map as #1.15, grid size 400,400,400, pixel 1.04, shown at level 0.1, step 1, values float32 Opened d9_ape as #2.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.012, step 1, values float32 Opened d9_ape1 as #2.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.012, step 1, values float32 Opened d9_ape2 as #2.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.012, step 1, values float32 Opened d9_ape3 as #2.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.012, step 1, values float32 Opened d9_pe as #2.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.012, step 1, values float32 Opened d9_e as #2.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.012, step 1, values float32 Opened d9_ape as #3.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0963, step 1, values float32 Opened d9_ape1 as #3.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0936, step 1, values float32 Opened d9_ape2 as #3.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0768, step 1, values float32 Opened d9_ape3 as #3.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0872, step 1, values float32 Opened d9_pe as #3.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0944, step 1, values float32 Opened d9_e as #3.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0736, step 1, values float32 Opened d9_J83_cl0 as #4.10, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.38, step 1, values float32 Opened d9_J84_cl1 as #4.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.38, step 1, values float32 Opened d9_J85_cl2 as #4.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.38, step 1, values float32 Opened d9_J86_cl3 as #4.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.38, step 1, values float32 Opened d9_J87_cl4 as #4.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.38, step 1, values float32 Opened d9_J88_cl5 as #4.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.38, step 1, values float32 Opened d9_J89_cl6 as #4.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.38, step 1, values float32 Opened d9_J90_cl7 as #4.7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.38, step 1, values float32 Opened d9_J91_cl8 as #4.8, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.38, step 1, values float32 Opened d9_J92_cl9 as #4.9, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.38, step 1, values float32 Opened d9_J83_cl0 as #5.10, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.33, step 1, values float32 Opened d9_J84_cl1 as #5.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.42, step 1, values float32 Opened d9_J85_cl2 as #5.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.38, step 1, values float32 Opened d9_J86_cl3 as #5.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.39, step 1, values float32 Opened d9_J87_cl4 as #5.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.38, step 1, values float32 Opened d9_J88_cl5 as #5.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.35, step 1, values float32 Opened d9_J89_cl6 as #5.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.38, step 1, values float32 Opened d9_J90_cl7 as #5.7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.39, step 1, values float32 Opened d9_J91_cl8 as #5.8, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.41, step 1, values float32 Opened d9_J92_cl9 as #5.9, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.37, step 1, values float32 Opened d10_ape as #10.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.011, step 1, values float32 Opened d10_pe as #10.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.011, step 1, values float32 Opened d10_e as #10.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.011, step 1, values float32 Opened d10_ape as #11.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0779, step 1, values float32 Opened d10_pe as #11.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0807, step 1, values float32 Opened d10_e as #11.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0701, step 1, values float32 Opened d10_J53_c0 as #12.10, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J54_c1 as #12.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J55_c2 as #12.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J56_c3 as #12.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J57_c4 as #12.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J58_c5 as #12.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J59_c6 as #12.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J60_c7 as #12.7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J61_c8 as #12.8, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J62_c9 as #12.9, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J53_c0 as #13.10, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.19, step 1, values float32 Opened d10_J54_c1 as #13.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.21, step 1, values float32 Opened d10_J55_c2 as #13.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.2, step 1, values float32 Opened d10_J56_c3 as #13.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.23, step 1, values float32 Opened d10_J57_c4 as #13.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.2, step 1, values float32 Opened d10_J58_c5 as #13.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.21, step 1, values float32 Opened d10_J59_c6 as #13.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.23, step 1, values float32 Opened d10_J60_c7 as #13.7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.24, step 1, values float32 Opened d10_J61_c8 as #13.8, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.21, step 1, values float32 Opened d10_J62_c9 as #13.9, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.23, step 1, values float32 Opened dE_J111_ape as #20.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.17, step 1, values float32 Opened dE_J112_ap as #20.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.17, step 1, values float32 Opened dE_J113_pe as #20.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.17, step 1, values float32 Opened dE_J124_e as #20.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.17, step 1, values float32 Opened dE_J111_ape as #21.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.25, step 1, values float32 Opened dE_J112_ap as #21.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.25, step 1, values float32 Opened dE_J113_pe as #21.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.25, step 1, values float32 Opened dE_J124_e as #21.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.25, step 1, values float32 Opened dE_J239_c0 as #23.10, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.07, step 1, values float32 Opened dE_J240_c1 as #23.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.07, step 1, values float32 Opened dE_J241_c2 as #23.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.07, step 1, values float32 Opened dE_J242_c3 as #23.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.07, step 1, values float32 Opened dE_J243_c4 as #23.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.07, step 1, values float32 Opened dE_J244_c5 as #23.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.07, step 1, values float32 Opened dE_J245_c6 as #23.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.07, step 1, values float32 Opened dE_J246_c7 as #23.7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.07, step 1, values float32 Opened dE_J247_c8 as #23.8, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.07, step 1, values float32 Opened dE_J248_c9 as #23.9, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.07, step 1, values float32 Log from Sun Sep 14 21:47:09 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open figure_H89.cxs Opened 8emm_map as #1.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.01, step 1, values float32 Opened 8b0x_map as #1.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.23, step 1, values float32 Opened 8cgk_map as #1.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0065, step 1, values float32 Opened 7bv8_map as #1.8, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.11, step 1, values float32 Opened 7o1a_map as #1.10, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.025, step 1, values float32 Opened 8cam_map as #1.13, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.01, step 1, values float32 Opened 5mdz_emd_3493.map as #1.15, grid size 400,400,400, pixel 1.04, shown at level 0.1, step 1, values float32 Opened d9_ape as #2.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.02, step 1, values float32 Opened d9_ape1 as #2.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.013, step 1, values float32 Opened d9_ape2 as #2.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.013, step 1, values float32 Opened d9_ape3 as #2.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.013, step 1, values float32 Opened d9_pe as #2.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.013, step 1, values float32 Opened d9_e as #2.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.009, step 1, values float32 Opened d9_ape as #3.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0963, step 1, values float32 Opened d9_ape1 as #3.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0936, step 1, values float32 Opened d9_ape2 as #3.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0768, step 1, values float32 Opened d9_ape3 as #3.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0872, step 1, values float32 Opened d9_pe as #3.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0944, step 1, values float32 Opened d9_e as #3.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0736, step 1, values float32 Opened d9_J83_cl0 as #4.10, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.4, step 1, values float32 Opened d9_J84_cl1 as #4.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at step 1, values float32 Opened d9_J85_cl2 as #4.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at step 1, values float32 Opened d9_J86_cl3 as #4.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at step 1, values float32 Opened d9_J87_cl4 as #4.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.4, step 1, values float32 Opened d9_J88_cl5 as #4.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.3, step 1, values float32 Opened d9_J89_cl6 as #4.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.4, step 1, values float32 Opened d9_J90_cl7 as #4.7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at step 1, values float32 Opened d9_J91_cl8 as #4.8, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.4, step 1, values float32 Opened d9_J92_cl9 as #4.9, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.4, step 1, values float32 Opened d9_J83_cl0 as #5.10, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.33, step 1, values float32 Opened d9_J84_cl1 as #5.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.42, step 1, values float32 Opened d9_J85_cl2 as #5.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.38, step 1, values float32 Opened d9_J86_cl3 as #5.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.39, step 1, values float32 Opened d9_J87_cl4 as #5.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.38, step 1, values float32 Opened d9_J88_cl5 as #5.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.35, step 1, values float32 Opened d9_J89_cl6 as #5.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.38, step 1, values float32 Opened d9_J90_cl7 as #5.7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.39, step 1, values float32 Opened d9_J91_cl8 as #5.8, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.41, step 1, values float32 Opened d9_J92_cl9 as #5.9, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.37, step 1, values float32 Opened d10_ape as #10.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.011, step 1, values float32 Opened d10_pe as #10.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.011, step 1, values float32 Opened d10_e as #10.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.011, step 1, values float32 Opened d10_ape as #11.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0779, step 1, values float32 Opened d10_pe as #11.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0807, step 1, values float32 Opened d10_e as #11.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0701, step 1, values float32 Opened d10_J53_c0 as #12.10, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J54_c1 as #12.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J55_c2 as #12.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J56_c3 as #12.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J57_c4 as #12.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J58_c5 as #12.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J59_c6 as #12.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J60_c7 as #12.7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J61_c8 as #12.8, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J62_c9 as #12.9, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J53_c0 as #13.10, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.19, step 1, values float32 Opened d10_J54_c1 as #13.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.21, step 1, values float32 Opened d10_J55_c2 as #13.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.2, step 1, values float32 Opened d10_J56_c3 as #13.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.23, step 1, values float32 Opened d10_J57_c4 as #13.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.2, step 1, values float32 Opened d10_J58_c5 as #13.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.21, step 1, values float32 Opened d10_J59_c6 as #13.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.23, step 1, values float32 Opened d10_J60_c7 as #13.7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.24, step 1, values float32 Opened d10_J61_c8 as #13.8, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.21, step 1, values float32 Opened d10_J62_c9 as #13.9, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.23, step 1, values float32 Opened dE_J111_ape as #20.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.22, step 1, values float32 Opened dE_J112_ap as #20.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.22, step 1, values float32 Opened dE_J113_pe as #20.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.23, step 1, values float32 Opened dE_J124_e as #20.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.17, step 1, values float32 Opened dE_J111_ape as #21.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.25, step 1, values float32 Opened dE_J112_ap as #21.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.25, step 1, values float32 Opened dE_J113_pe as #21.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.25, step 1, values float32 Opened dE_J124_e as #21.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.25, step 1, values float32 Opened dE_J239_c0 as #23.10, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.08, step 1, values float32 Opened dE_J240_c1 as #23.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.08, step 1, values float32 Opened dE_J241_c2 as #23.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.08, step 1, values float32 Opened dE_J242_c3 as #23.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.08, step 1, values float32 Opened dE_J243_c4 as #23.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.08, step 1, values float32 Opened dE_J244_c5 as #23.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.08, step 1, values float32 Opened dE_J245_c6 as #23.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.08, step 1, values float32 Opened dE_J246_c7 as #23.7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.08, step 1, values float32 Opened dE_J247_c8 as #23.8, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.08, step 1, values float32 Opened dE_J248_c9 as #23.9, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.08, step 1, values float32 Log from Mon Aug 25 21:17:17 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open figure_D2449_new.cxs Opened 8emm_map as #1.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.01, step 1, values float32 Opened 8b0x_map as #1.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.23, step 1, values float32 Opened 8cgk_map as #1.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0065, step 1, values float32 Opened 7bv8_map as #1.8, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.11, step 1, values float32 Opened 7o1a_map as #1.10, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.025, step 1, values float32 Opened 8cam_map as #1.13, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.01, step 1, values float32 Opened d9_ape as #2.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.02, step 1, values float32 Opened d9_ape1 as #2.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.013, step 1, values float32 Opened d9_ape2 as #2.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.013, step 1, values float32 Opened d9_ape3 as #2.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.013, step 1, values float32 Opened d9_pe as #2.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.013, step 1, values float32 Opened d9_e as #2.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.009, step 1, values float32 Opened d9_ape as #3.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0963, step 1, values float32 Opened d9_ape1 as #3.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0936, step 1, values float32 Opened d9_ape2 as #3.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0768, step 1, values float32 Opened d9_ape3 as #3.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0872, step 1, values float32 Opened d9_pe as #3.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0944, step 1, values float32 Opened d9_e as #3.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0736, step 1, values float32 Opened d9_J83_cl0 as #4.10, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.4, step 1, values float32 Opened d9_J84_cl1 as #4.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.4, step 1, values float32 Opened d9_J85_cl2 as #4.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.4, step 1, values float32 Opened d9_J86_cl3 as #4.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.4, step 1, values float32 Opened d9_J87_cl4 as #4.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.4, step 1, values float32 Opened d9_J88_cl5 as #4.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.3, step 1, values float32 Opened d9_J89_cl6 as #4.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.4, step 1, values float32 Opened d9_J90_cl7 as #4.7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.4, step 1, values float32 Opened d9_J91_cl8 as #4.8, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.4, step 1, values float32 Opened d9_J92_cl9 as #4.9, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.4, step 1, values float32 Opened d9_J83_cl0 as #5.10, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.33, step 1, values float32 Opened d9_J84_cl1 as #5.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.42, step 1, values float32 Opened d9_J85_cl2 as #5.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.38, step 1, values float32 Opened d9_J86_cl3 as #5.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.39, step 1, values float32 Opened d9_J87_cl4 as #5.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.38, step 1, values float32 Opened d9_J88_cl5 as #5.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.35, step 1, values float32 Opened d9_J89_cl6 as #5.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.38, step 1, values float32 Opened d9_J90_cl7 as #5.7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.39, step 1, values float32 Opened d9_J91_cl8 as #5.8, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.41, step 1, values float32 Opened d9_J92_cl9 as #5.9, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.37, step 1, values float32 Opened d10_ape as #10.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.011, step 1, values float32 Opened d10_pe as #10.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.011, step 1, values float32 Opened d10_e as #10.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.011, step 1, values float32 Opened d10_ape as #11.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0779, step 1, values float32 Opened d10_pe as #11.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0807, step 1, values float32 Opened d10_e as #11.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0701, step 1, values float32 Opened d10_J53_c0 as #12.10, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J54_c1 as #12.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J55_c2 as #12.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J56_c3 as #12.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J57_c4 as #12.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J58_c5 as #12.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J59_c6 as #12.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J60_c7 as #12.7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J61_c8 as #12.8, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J62_c9 as #12.9, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.35, step 1, values float32 Opened d10_J53_c0 as #13.10, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.19, step 1, values float32 Opened d10_J54_c1 as #13.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.21, step 1, values float32 Opened d10_J55_c2 as #13.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.2, step 1, values float32 Opened d10_J56_c3 as #13.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.23, step 1, values float32 Opened d10_J57_c4 as #13.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.2, step 1, values float32 Opened d10_J58_c5 as #13.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.21, step 1, values float32 Opened d10_J59_c6 as #13.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.23, step 1, values float32 Opened d10_J60_c7 as #13.7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.24, step 1, values float32 Opened d10_J61_c8 as #13.8, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.21, step 1, values float32 Opened d10_J62_c9 as #13.9, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.23, step 1, values float32 Opened dE_J111_ape as #20.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.22, step 1, values float32 Opened dE_J112_ap as #20.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.22, step 1, values float32 Opened dE_J113_pe as #20.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.23, step 1, values float32 Opened dE_J124_e as #20.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.17, step 1, values float32 Opened dE_J111_ape as #21.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.25, step 1, values float32 Opened dE_J112_ap as #21.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.25, step 1, values float32 Opened dE_J113_pe as #21.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.25, step 1, values float32 Opened dE_J124_e as #21.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.25, step 1, values float32 Opened dE_J239_c0 as #23.10, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.08, step 1, values float32 Opened dE_J240_c1 as #23.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.08, step 1, values float32 Opened dE_J241_c2 as #23.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.08, step 1, values float32 Opened dE_J242_c3 as #23.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.08, step 1, values float32 Opened dE_J243_c4 as #23.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.08, step 1, values float32 Opened dE_J244_c5 as #23.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.08, step 1, values float32 Opened dE_J245_c6 as #23.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.08, step 1, values float32 Opened dE_J246_c7 as #23.7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.08, step 1, values float32 Opened dE_J247_c8 as #23.8, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.08, step 1, values float32 Opened dE_J248_c9 as #23.9, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.08, step 1, values float32 Log from Sun Aug 17 22:37:00 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open figure_A-loop_new.cxs Opened 8emm_map as #1.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.015, step 1, values float32 Opened 8b0x_map as #1.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.23, step 1, values float32 Opened 8cgk_map as #1.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.01, step 1, values float32 Opened 7bv8_map as #1.8, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.11, step 1, values float32 Opened 7o1a_map as #1.10, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.025, step 1, values float32 Opened 8cam_map as #1.13, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.01, step 1, values float32 Opened d9_ape as #2.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.02, step 1, values float32 Opened d9_ape1 as #2.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.016, step 1, values float32 Opened d9_ape2 as #2.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.014, step 1, values float32 Opened d9_ape3 as #2.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.014, step 1, values float32 Opened d9_pe as #2.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.016, step 1, values float32 Opened d9_e as #2.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.012, step 1, values float32 Opened d9_ape as #3.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0963, step 1, values float32 Opened d9_ape1 as #3.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0936, step 1, values float32 Opened d9_ape2 as #3.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0768, step 1, values float32 Opened d9_ape3 as #3.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0872, step 1, values float32 Opened d9_pe as #3.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0944, step 1, values float32 Opened d9_e as #3.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0736, step 1, values float32 Opened d9_J83_cl0 as #4.10, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d9_J84_cl1 as #4.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d9_J85_cl2 as #4.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d9_J86_cl3 as #4.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d9_J87_cl4 as #4.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d9_J88_cl5 as #4.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d9_J89_cl6 as #4.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d9_J90_cl7 as #4.7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d9_J91_cl8 as #4.8, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d9_J92_cl9 as #4.9, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d9_J83_cl0 as #5.10, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.33, step 1, values float32 Opened d9_J84_cl1 as #5.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.42, step 1, values float32 Opened d9_J85_cl2 as #5.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.38, step 1, values float32 Opened d9_J86_cl3 as #5.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.39, step 1, values float32 Opened d9_J87_cl4 as #5.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.38, step 1, values float32 Opened d9_J88_cl5 as #5.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.35, step 1, values float32 Opened d9_J89_cl6 as #5.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.38, step 1, values float32 Opened d9_J90_cl7 as #5.7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.39, step 1, values float32 Opened d9_J91_cl8 as #5.8, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.41, step 1, values float32 Opened d9_J92_cl9 as #5.9, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.37, step 1, values float32 Opened d10_ape as #10.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.015, step 1, values float32 Opened d10_pe as #10.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.015, step 1, values float32 Opened d10_e as #10.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.012, step 1, values float32 Opened d10_ape as #11.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0779, step 1, values float32 Opened d10_pe as #11.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0807, step 1, values float32 Opened d10_e as #11.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0701, step 1, values float32 Opened d10_J53_c0 as #12.10, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d10_J54_c1 as #12.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d10_J55_c2 as #12.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d10_J56_c3 as #12.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d10_J57_c4 as #12.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d10_J58_c5 as #12.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d10_J59_c6 as #12.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d10_J60_c7 as #12.7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d10_J61_c8 as #12.8, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d10_J62_c9 as #12.9, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d10_J53_c0 as #13.10, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.19, step 1, values float32 Opened d10_J54_c1 as #13.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.21, step 1, values float32 Opened d10_J55_c2 as #13.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.2, step 1, values float32 Opened d10_J56_c3 as #13.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.23, step 1, values float32 Opened d10_J57_c4 as #13.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.2, step 1, values float32 Opened d10_J58_c5 as #13.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.21, step 1, values float32 Opened d10_J59_c6 as #13.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.23, step 1, values float32 Opened d10_J60_c7 as #13.7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.24, step 1, values float32 Opened d10_J61_c8 as #13.8, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.21, step 1, values float32 Opened d10_J62_c9 as #13.9, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.23, step 1, values float32 Opened dE_J111_ape as #20.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.22, step 1, values float32 Opened dE_J112_ap as #20.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.22, step 1, values float32 Opened dE_J113_pe as #20.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.23, step 1, values float32 Opened dE_J124_e as #20.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.17, step 1, values float32 Opened dE_J111_ape as #21.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.4, step 1, values float32 Opened dE_J112_ap as #21.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.4, step 1, values float32 Opened dE_J113_pe as #21.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.4, step 1, values float32 Opened dE_J124_e as #21.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.4, step 1, values float32 Opened dE_J239_c0 as #23.10, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.1, step 1, values float32 Opened dE_J240_c1 as #23.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.1, step 1, values float32 Opened dE_J241_c2 as #23.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.1, step 1, values float32 Opened dE_J242_c3 as #23.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.1, step 1, values float32 Opened dE_J243_c4 as #23.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.1, step 1, values float32 Opened dE_J244_c5 as #23.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.1, step 1, values float32 Opened dE_J245_c6 as #23.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.1, step 1, values float32 Opened dE_J246_c7 as #23.7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.1, step 1, values float32 Opened dE_J247_c8 as #23.8, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.1, step 1, values float32 Opened dE_J248_c9 as #23.9, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.1, step 1, values float32 Log from Fri Jul 4 17:41:34 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/dalar193/wd/deltaRibosomes/figure_A-loop_new.cxs Opened 8emm_map as #1.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.015, step 1, values float32 Opened 8b0x_map as #1.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.23, step 1, values float32 Opened 8cgk_map as #1.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.01, step 1, values float32 Opened 7bv8_map as #1.8, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.11, step 1, values float32 Opened 7o1a_map as #1.10, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.025, step 1, values float32 Opened 8cam_map as #1.13, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.01, step 1, values float32 Opened d9_ape as #2.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.02, step 1, values float32 Opened d9_ape1 as #2.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.016, step 1, values float32 Opened d9_ape2 as #2.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.014, step 1, values float32 Opened d9_ape3 as #2.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.014, step 1, values float32 Opened d9_pe as #2.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.016, step 1, values float32 Opened d9_e as #2.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.012, step 1, values float32 Opened d9_ape as #3.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0963, step 1, values float32 Opened d9_ape1 as #3.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0936, step 1, values float32 Opened d9_ape2 as #3.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0768, step 1, values float32 Opened d9_ape3 as #3.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0872, step 1, values float32 Opened d9_pe as #3.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0944, step 1, values float32 Opened d9_e as #3.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0736, step 1, values float32 Opened d9_J83_cl0 as #4.10, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d9_J84_cl1 as #4.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d9_J85_cl2 as #4.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d9_J86_cl3 as #4.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d9_J87_cl4 as #4.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d9_J88_cl5 as #4.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d9_J89_cl6 as #4.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d9_J90_cl7 as #4.7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d9_J91_cl8 as #4.8, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d9_J92_cl9 as #4.9, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d9_J83_cl0 as #5.10, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.33, step 1, values float32 Opened d9_J84_cl1 as #5.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.42, step 1, values float32 Opened d9_J85_cl2 as #5.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.38, step 1, values float32 Opened d9_J86_cl3 as #5.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.39, step 1, values float32 Opened d9_J87_cl4 as #5.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.38, step 1, values float32 Opened d9_J88_cl5 as #5.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.35, step 1, values float32 Opened d9_J89_cl6 as #5.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.38, step 1, values float32 Opened d9_J90_cl7 as #5.7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.39, step 1, values float32 Opened d9_J91_cl8 as #5.8, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.41, step 1, values float32 Opened d9_J92_cl9 as #5.9, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.37, step 1, values float32 Opened d10_ape as #10.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.015, step 1, values float32 Opened d10_pe as #10.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.015, step 1, values float32 Opened d10_e as #10.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.012, step 1, values float32 Opened d10_ape as #11.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0779, step 1, values float32 Opened d10_pe as #11.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0807, step 1, values float32 Opened d10_e as #11.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0701, step 1, values float32 Opened d10_J53_c0 as #12.10, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d10_J54_c1 as #12.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d10_J55_c2 as #12.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.4, step 1, values float32 Opened d10_J56_c3 as #12.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d10_J57_c4 as #12.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d10_J58_c5 as #12.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d10_J59_c6 as #12.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d10_J60_c7 as #12.7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d10_J61_c8 as #12.8, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d10_J62_c9 as #12.9, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.5, step 1, values float32 Opened d10_J53_c0 as #13.10, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.19, step 1, values float32 Opened d10_J54_c1 as #13.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.21, step 1, values float32 Opened d10_J55_c2 as #13.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.2, step 1, values float32 Opened d10_J56_c3 as #13.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.23, step 1, values float32 Opened d10_J57_c4 as #13.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.2, step 1, values float32 Opened d10_J58_c5 as #13.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.21, step 1, values float32 Opened d10_J59_c6 as #13.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.23, step 1, values float32 Opened d10_J60_c7 as #13.7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.24, step 1, values float32 Opened d10_J61_c8 as #13.8, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.21, step 1, values float32 Opened d10_J62_c9 as #13.9, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 1.23, step 1, values float32 Opened dE_J111_ape as #20.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.22, step 1, values float32 Opened dE_J112_ap as #20.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.22, step 1, values float32 Opened dE_J113_pe as #20.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.23, step 1, values float32 Opened dE_J124_e as #20.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.17, step 1, values float32 Opened dE_J111_ape as #21.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.4, step 1, values float32 Opened dE_J112_ap as #21.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.4, step 1, values float32 Opened dE_J113_pe as #21.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.4, step 1, values float32 Opened dE_J124_e as #21.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.4, step 1, values float32 Opened dE_J239_c0 as #23.10, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.1, step 1, values float32 Opened dE_J240_c1 as #23.1, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.1, step 1, values float32 Opened dE_J241_c2 as #23.2, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.1, step 1, values float32 Opened dE_J242_c3 as #23.3, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.1, step 1, values float32 Opened dE_J243_c4 as #23.4, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.1, step 1, values float32 Opened dE_J244_c5 as #23.5, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.1, step 1, values float32 Opened dE_J245_c6 as #23.6, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.1, step 1, values float32 Opened dE_J246_c7 as #23.7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.1, step 1, values float32 Opened dE_J247_c8 as #23.8, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.1, step 1, values float32 Opened dE_J248_c9 as #23.9, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.1, step 1, values float32 Log from Thu Jul 3 21:26:40 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/dalar193/wd/deltaRibosomes/figure_with_maps.cxs Opened 8b0x_map as #1.3, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.23, step 1, values float32 Opened 8cgk_map as #1.6, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.004, step 1, values float32 Opened 7bv8_map as #1.8, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.0847, step 1, values float32 Opened 7o1a_map as #1.10, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.012, step 1, values float32 Opened 8emm_map as #1.1, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.02, step 1, values float32 Opened d9_ape as #2.1, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.025, step 1, values float32 Opened d9_ape1 as #2.2, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.016, step 1, values float32 Opened d9_ape2 as #2.3, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.014, step 1, values float32 Opened d9_ape3 as #2.4, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.014, step 1, values float32 Opened d9_pe as #2.5, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.016, step 1, values float32 Opened d9_e as #2.6, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.012, step 1, values float32 Opened d9_ape as #3.1, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.0963, step 1, values float32 Opened d9_ape1 as #3.2, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.032, step 1, values float32 Opened d9_ape2 as #3.3, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.032, step 1, values float32 Opened d9_ape3 as #3.4, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.032, step 1, values float32 Opened d9_pe as #3.5, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.032, step 1, values float32 Opened d9_e as #3.6, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.032, step 1, values float32 Opened d9_J83_cl0 as #4.10, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.4, step 1, values float32 Opened d9_J84_cl1 as #4.1, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.5, step 1, values float32 Opened d9_J85_cl2 as #4.2, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.47, step 1, values float32 Opened d9_J86_cl3 as #4.3, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.5, step 1, values float32 Opened d9_J87_cl4 as #4.4, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.4, step 1, values float32 Opened d9_J88_cl5 as #4.5, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.48, step 1, values float32 Opened d9_J89_cl6 as #4.6, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.5, step 1, values float32 Opened d9_J90_cl7 as #4.7, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.5, step 1, values float32 Opened d9_J91_cl8 as #4.8, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.55, step 1, values float32 Opened d9_J92_cl9 as #4.9, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.52, step 1, values float32 Opened d9_J83_cl0 as #5.10, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.44, step 1, values float32 Opened d9_J84_cl1 as #5.1, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.44, step 1, values float32 Opened d9_J85_cl2 as #5.2, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.44, step 1, values float32 Opened d9_J86_cl3 as #5.3, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.44, step 1, values float32 Opened d9_J87_cl4 as #5.4, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.44, step 1, values float32 Opened d9_J88_cl5 as #5.5, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.44, step 1, values float32 Opened d9_J89_cl6 as #5.6, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.44, step 1, values float32 Opened d9_J90_cl7 as #5.7, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.44, step 1, values float32 Opened d9_J91_cl8 as #5.8, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.44, step 1, values float32 Opened d9_J92_cl9 as #5.9, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.44, step 1, values float32 Opened d10_ape as #10.1, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.015, step 1, values float32 Opened d10_pe as #10.2, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.015, step 1, values float32 Opened d10_e as #10.3, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.012, step 1, values float32 Opened d10_ape as #11.1, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.032, step 1, values float32 Opened d10_pe as #11.2, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.032, step 1, values float32 Opened d10_e as #11.3, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.032, step 1, values float32 Opened d10_J53_c0 as #12.10, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.36, step 1, values float32 Opened d10_J54_c1 as #12.1, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.4, step 1, values float32 Opened d10_J55_c2 as #12.2, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.41, step 1, values float32 Opened d10_J56_c3 as #12.3, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.43, step 1, values float32 Opened d10_J57_c4 as #12.4, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.42, step 1, values float32 Opened d10_J58_c5 as #12.5, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.42, step 1, values float32 Opened d10_J59_c6 as #12.6, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.43, step 1, values float32 Opened d10_J60_c7 as #12.7, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.44, step 1, values float32 Opened d10_J61_c8 as #12.8, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.41, step 1, values float32 Opened d10_J62_c9 as #12.9, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.42, step 1, values float32 Opened d10_J53_c0 as #13.10, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.44, step 1, values float32 Opened d10_J54_c1 as #13.1, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.44, step 1, values float32 Opened d10_J55_c2 as #13.2, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.44, step 1, values float32 Opened d10_J56_c3 as #13.3, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.44, step 1, values float32 Opened d10_J57_c4 as #13.4, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.44, step 1, values float32 Opened d10_J58_c5 as #13.5, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.44, step 1, values float32 Opened d10_J59_c6 as #13.6, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.44, step 1, values float32 Opened d10_J60_c7 as #13.7, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.44, step 1, values float32 Opened d10_J61_c8 as #13.8, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.44, step 1, values float32 Opened d10_J62_c9 as #13.9, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.44, step 1, values float32 Opened dE_J111_ape as #20.1, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.22, step 1, values float32 Opened dE_J112_ap as #20.2, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.22, step 1, values float32 Opened dE_J113_pe as #20.3, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.23, step 1, values float32 Opened dE_J124_e as #20.4, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.17, step 1, values float32 Opened dE_J111_ape as #21.1, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.16, step 1, values float32 Opened dE_J112_ap as #21.2, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.16, step 1, values float32 Opened dE_J113_pe as #21.3, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.16, step 1, values float32 Opened dE_J124_e as #21.4, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.16, step 1, values float32 Opened delE50S_homogen_J36_0.70469Apix.mrc as #7, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.309, step 1, values float32 Log from Fri Apr 19 16:41:09 2024 Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle > mousemode middleMode ""center or translate"" 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 > set bgColor white > default stick Unknown command: default stick > style stick Changed 0 atom styles > volume style mesh No volumes specified > open > /Users/dalar193/wd/deltaRibosomes/aligned_maps/EMD22586_7k00_x1.0067.mrc id > 1.1 name 7k00_map Opened 7k00_map as #1, grid size 391,421,391, pixel 0.705,0.705,0.705, shown at level 0.046, step 2, values float32 > open /Users/dalar193/wd/deltaRibosomes/aligned_maps/7k00_x1.0067_LSQ-23S.pdb > id 1.2 name 7k00 Summary of feedback from opening /Users/dalar193/wd/deltaRibosomes/aligned_maps/7k00_x1.0067_LSQ-23S.pdb --- warnings | Start residue of secondary structure not found: SHEET 1 AC5 2 VAL X 3 LYS X 5 0 Start residue of secondary structure not found: SHEET 2 AC5 2 VAL X 17 VAL X 19 -1 Start residue of secondary structure not found: SHEET 1 AC6 2 LEU X 34 LYS X 36 0 Start residue of secondary structure not found: SHEET 2 AC6 2 ALA X 61 ARG X 63 -1 Start residue of secondary structure not found: SHEET 1 AC7 4 ARG X 101 LEU X 105 0 43 messages similar to the above omitted End residue of secondary structure not found: SHEET 1 AD9 3 ARG B 95 LYS B 99 0 Start residue of secondary structure not found: SHEET 2 AD9 3 VAL B 102 SER B 106 -1 Start residue of secondary structure not found: SHEET 3 AD9 3 VAL B 113 GLN B 116 -1 Start residue of secondary structure not found: SHEET 1 AE1 3 GLN C 18 ASN C 20 0 Start residue of secondary structure not found: SHEET 2 AE1 3 GLN C 2 ILE C 4 -1 Start residue of secondary structure not found: SHEET 3 AE1 3 VAL C 37 PRO C 38 -1 24 messages similar to the above omitted End residue of secondary structure not found: SHEET 1 AE8 3 VAL F 89 VAL F 90 0 Start residue of secondary structure not found: SHEET 2 AE8 3 THR F 121 VAL F 122 1 Start residue of secondary structure not found: SHEET 3 AE8 3 LYS F 141 ILE F 142 1 Start residue of secondary structure not found: SHEET 1 AE9 4 LYS G 62 ILE G 65 0 Start residue of secondary structure not found: SHEET 2 AE9 4 VAL G 101 ASP G 106 -1 Start residue of secondary structure not found: SHEET 3 AE9 4 PHE G 31 ALA G 35 -1 7 messages similar to the above omitted End residue of secondary structure not found: SHEET 1 AF3 4 VAL I 47 SER I 52 0 Start residue of secondary structure not found: SHEET 2 AF3 4 ILE I 35 ILE I 40 -1 Start residue of secondary structure not found: SHEET 3 AF3 4 ARG I 25 ARG I 30 -1 Start residue of secondary structure not found: SHEET 4 AF3 4 SER I 91 ASP I 93 1 End residue of secondary structure not found: SHEET 1 AF4 4 LYS L 10 VAL L 14 0 Start residue of secondary structure not found: SHEET 2 AF4 4 TYR L 2 SER L 7 -1 Start residue of secondary structure not found: SHEET 3 AF4 4 VAL L 38 ALA L 42 -1 Start residue of secondary structure not found: SHEET 4 AF4 4 VAL L 47 ILE L 49 -1 Start residue of secondary structure not found: SHEET 1 AF5 4 THR L 19 LEU L 22 0 Start residue of secondary structure not found: SHEET 2 AF5 4 TRP L 92 SER L 102 -1 37 messages similar to the above omitted End residue of secondary structure not found: SHEET 3 AG7 4 ARG Q 77 GLU Q 83 -1 Start residue of secondary structure not found: SHEET 4 AG7 4 HIS Q 46 ALA Q 47 1 Start residue of secondary structure not found: SHEET 1 AG8 2 VAL R 13 ARG R 18 0 Start residue of secondary structure not found: SHEET 2 AG8 2 ALA R 24 PHE R 29 -1 Start residue of secondary structure not found: SHEET 1 AG9 2 LEU R 33 VAL R 40 0 Start residue of secondary structure not found: SHEET 2 AG9 2 ARG R 45 SER R 52 -1 21 messages similar to the above omitted Chain information for 7k00 #2 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available 3 | No description available 4 | No description available 5 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available g | No description available h | No description available i | No description available j | No description available k | No description available l | No description available m | No description available n | No description available o | No description available p | No description available q | No description available r | No description available s | No description available t | No description available u | No description available v | No description available w | No description available x | No description available y | No description available z | No description available [deleted to fit within ticket limits] > color #25.5/a:2494 #25.5/a:2493@O3' magenta target a > color #25.7/a:2494 #25.7/a:2493@O3' magenta target a > color #6.1/a:2494@O3' light gray target a > color #6.2/a:2494@O3' light gray target a > color #6.7/a:2494@O3' light gray target a > color #14.3/a:2494@O3' light gray target a > color #14.9/a:2494@O3' light gray target a > color #25.5/a:2494@O3' light gray target a > color #25.7/a:2494@O3' light gray target a > hide #!1.2 models > hide #!1.16 models > hide #!6.* models > hide #!14.* models > hide #!25.* models > view H89 > show #!1.2 models > save /Users/dalar193/Desktop/H89_U2491/H89-8EMM.png width 580 height 800 > supersample 4 > hide #!1.2 models > transparency #1.2 80 target c > hide #1.2 > show #!1.2 models > show #!1.16 models > save /Users/dalar193/Desktop/H89_U2491/H89-5MDZ.png width 580 height 800 > supersample 4 > hide #!1.16 models > show #!6.10 models > save /Users/dalar193/Desktop/H89_U2491/H89-del9-class0.png width 580 height > 800 supersample 4 > hide #!6.10 models > show #!6.1 models > save /Users/dalar193/Desktop/H89_U2491/H89-del9-class1.png width 580 height > 800 supersample 4 > hide #!6.1 models > show #!6.2 models > save /Users/dalar193/Desktop/H89_U2491/H89-del9-class2.png width 580 height > 800 supersample 4 > hide #!6.2 models > show #!6.3 models > save /Users/dalar193/Desktop/H89_U2491/H89-del9-class3.png width 580 height > 800 supersample 4 > hide #!6.3 models > show #!6.4 models > save /Users/dalar193/Desktop/H89_U2491/H89-del9-class4.png width 580 height > 800 supersample 4 > hide #!6.4 models > show #!6.5 models > save /Users/dalar193/Desktop/H89_U2491/H89-del9-class5.png width 580 height > 800 supersample 4 > hide #!6.5 models > show #!6.6 models > save /Users/dalar193/Desktop/H89_U2491/H89-del9-class6.png width 580 height > 800 supersample 4 > hide #!6.6 models > show #!6.7 models > save /Users/dalar193/Desktop/H89_U2491/H89-del9-class7.png width 580 height > 800 supersample 4 > hide #!6.7 models > show #!6.8 models > save /Users/dalar193/Desktop/H89_U2491/H89-del9-class8.png width 580 height > 800 supersample 4 > hide #!6.8 models > show #!6.9 models > save /Users/dalar193/Desktop/H89_U2491/H89-del9-class9.png width 580 height > 800 supersample 4 > hide #!6.9 models > show #!14.10 models > save /Users/dalar193/Desktop/H89_U2491/H89-del10-class0.png width 580 height > 800 supersample 4 > hide #!14.10 models > show #!14.1 models > save /Users/dalar193/Desktop/H89_U2491/H89-del10-class1.png width 580 height > 800 supersample 4 > hide #!14.1 models > show #!14.2 models > save /Users/dalar193/Desktop/H89_U2491/H89-del10-class2.png width 580 height > 800 supersample 4 > hide #!14.2 models > show #!14.3 models > save /Users/dalar193/Desktop/H89_U2491/H89-del10-class3.png width 580 height > 800 supersample 4 > hide #!14.3 models > show #!14.4 models > save /Users/dalar193/Desktop/H89_U2491/H89-del10-class4.png width 580 height > 800 supersample 4 > hide #!14.4 models > show #!14.5 models > save /Users/dalar193/Desktop/H89_U2491/H89-del10-class5.png width 580 height > 800 supersample 4 > hide #!14.5 models > show #!14.6 models > save /Users/dalar193/Desktop/H89_U2491/H89-del10-class6.png width 580 height > 800 supersample 4 > hide #!14.6 models > show #!14.7 models > save /Users/dalar193/Desktop/H89_U2491/H89-del10-class7.png width 580 height > 800 supersample 4 > hide #!14.7 models > show #!14.8 models > save /Users/dalar193/Desktop/H89_U2491/H89-del10-class8.png width 580 height > 800 supersample 4 > hide #!14.8 models > show #!14.9 models > save /Users/dalar193/Desktop/H89_U2491/H89-del10-class9.png width 580 height > 800 supersample 4 > hide #!14.9 models > show #!25.10 models > save /Users/dalar193/Desktop/H89_U2491/H89-delE-class0.png width 580 height > 800 supersample 4 > hide #!25.10 models > show #!25.1 models > save /Users/dalar193/Desktop/H89_U2491/H89-delE-class1.png width 580 height > 800 supersample 4 > hide #!25.1 models > show #!25.2 models > save /Users/dalar193/Desktop/H89_U2491/H89-delE-class2.png width 580 height > 800 supersample 4 > hide #!25.2 models > show #!25.3 models > save /Users/dalar193/Desktop/H89_U2491/H89-delE-class3.png width 580 height > 800 supersample 4 > hide #!25.3 models > show #!25.4 models > save /Users/dalar193/Desktop/H89_U2491/H89-delE-class4.png width 580 height > 800 supersample 4 > hide #!25.4 models > show #!25.5 models > save /Users/dalar193/Desktop/H89_U2491/H89-delE-class5.png width 580 height > 800 supersample 4 > hide #!25.5 models > show #!25.6 models > save /Users/dalar193/Desktop/H89_U2491/H89-delE-class6.png width 580 height > 800 supersample 4 > hide #!25.6 models > show #!25.7 models > save /Users/dalar193/Desktop/H89_U2491/H89-delE-class7.png width 580 height > 800 supersample 4 > hide #!25.7 models > show #!25.8 models > save /Users/dalar193/Desktop/H89_U2491/H89-delE-class8.png width 580 height > 800 supersample 4 > hide #!25.8 models > show #!25.9 models > save /Users/dalar193/Desktop/H89_U2491/H89-delE-class9.png width 580 height > 800 supersample 4 > hide #!25.9 models > transparency #1.2 0 target c > show #1.2/a:2491,2457,2498,2451,2449-2463,2487-2501 > show #1.2/a:2518 & sidechain > show #1.2/v:1-5 > show #1.2/a:6231,8885 > color #1.2/a:MG tomato > color #1.2/a:HOH royal blue > show #!1.2 models > save /Users/dalar193/Desktop/H89_U2491/H89-8EMM.png width 580 height 800 > supersample 4 > hide #!1.2 models > show #!6.4 models > show #!1.2 models > hide #!1.2 models > show #!1.2 models > hide #!1.2 models > save /Users/dalar193/wd/deltaRibosomes/figure_H89.cxs ——— End of log from Mon Aug 25 21:17:17 2025 ——— opened ChimeraX session > show #!20.1 models > hide #!6.4 models > hide #7 models > close #7 > volume surfaceSmoothing Missing ""surfaceSmoothing"" keyword's argument > volume style surface > lighting soft > volume #20.1 level 0.1 > volume #20.1 level 0.15 > volume #20.1 level 0.17 > volume #20.1 level 0.16 > volume #20.2 level 0.16 > volume #20.3 level 0.16 > volume #20.* level 0.17 > show #!20.4 models > hide #!20.3 models > show #!20.3 models > hide #!20.4 models > show #!20.2 models > hide #!20.3 models > hide #!20.2 models > show #!23.1 models > hide #!20.1 models > show #!23.2 models > hide #!23.1 models > volume #23.* unzone Expected a keyword > volume unzone #23.* > volume transparency 0 > color #20.2 dark grey > hide #!23.2 models > show #!23.2 models > color #20.2 dim gray > color #23.2 dim gray > color #23.2 gray > color #23.2#20.2 gray > color #23.2#20.2 yellow > color #23.2 yellow > volume #23.2 color yellow > volume #23.2 color red > show #!20.2 models > show #!20.1 models > volume #20.2 color red > hide #!23.2 models > volume #20.2 dimTransparency gray Invalid ""dimTransparency"" argument: Expected true or false (or 1 or 0) > volume #20.2 color dim gray > volume #20.2 color gray > hide #!20.2 models > show #!20.2 models > show #!23.2 models > hide #!23.2 models > show #!23.2 models > volume #23.2 color gray > hide #!23.2 models > show #!23.2 models > volume #23.2 color silver > hide #!20.2 models > hide #!20.1 models > show #!20.2 models > hide #!20.2 models > show #!20.2 models > show #!20.1 models > volume color gray > hide #!20.2 models > hide #!20.1 models > show #!23.3 models > hide #!23.2 models > show #!23.4 models > hide #!23.3 models > show #!25.1 models > hide #!25.1 models > show #!25.1 models > hide #!23.4 models > hide #!25.1 models > show #!23.2 models > hide #!23.2 models > show #!22.3 models > hide #!22.3 models > show #!21.2 models > hide #!21.2 models > show #!21.2 models > hide #!21.2 models > volume unzone > show #!22.2 models > hide #!22.2 models > show #!21.2 models > hide #!21.2 models > show #!20.3 models > hide #!20.3 models > show #!20.1 models > show #!23.1 models > volume #20.1 color green > volume #20.1 color cyan > volume #23.* level 0.08 > volume #23.* level 0.09 > volume #23.* level 0.07 > show #!23.2 models > hide #!23.1 models > show #!23.3 models > hide #!23.2 models > show #!23.4 models > hide #!23.3 models > show #!23.5 models > hide #!23.4 models > show #!23.6 models > hide #!23.5 models > show #!23.7 models > hide #!23.6 models > show #!23.8 models > hide #!23.7 models > show #!23.9 models > hide #!23.8 models > show #!23.10 models > hide #!23.9 models > hide #!23.10 models > show #!23.6 models > hide #!23.6 models > show #!23.5 models > hide #!23.5 models > show #!23.4 models > hide #!23.4 models > show #!23.3 models > hide #!23.3 models > show #!23.3 models > hide #!23.3 models > show #!23.3 models > hide #!23.3 models > show #!12.1 models > hide #!12.1 models > show #!12.1 models > show #!12.2 models > hide #!12.1 models > show #!12.3 models > hide #!12.2 models > show #!12.4 models > hide #!12.4 models > hide #!12.3 models > show #!12.4 models > show #!12.5 models > hide #!12.4 models > show #!12.6 models > hide #!12.5 models > show #!12.7 models > hide #!12.6 models > show #!12.8 models > hide #!12.7 models > show #!12.9 models > hide #!12.8 models > show #!12.10 models > hide #!12.9 models > hide #!12.10 models > show #!10.1 models > show #!11.1 models > hide #!11 models > hide #!11.1 models > show #!11 models > show #!10.2 models > hide #!10.1 models > show #!10.3 models > hide #!10.2 models > hide #!10.3 models > show #!4.1 models > volume #4.4 level 0.35 > volume #4.4 level 0.4 > volume #4.1 level 0.35 > volume #4.1 level 0.4 > volume #4.1 level 0.38 > volume #4.1 level 0.36 > volume #4.* level 0.36 > hide #!4.1 models > show #!4.2 models > hide #!4.2 models > show #!4.3 models > hide #!4.3 models > show #!4.4 models > hide #!4.4 models > show #!4.5 models > hide #!4.5 models > show #!4.6 models > hide #!4.6 models > show #!4.7 models > hide #!4.7 models > show #!4.8 models > hide #!4.8 models > show #!4.9 models > hide #!4.9 models > show #!4.10 models > volume #4.* level 0.37 > volume #4.* level 0.38 [Repeated 1 time(s)] > hide #!4.10 models > show #!2.1 models > hide #!2.1 models > show #!2.2 models > volume #2.2 level 0.012 > volume #2.2 level 0.011 > volume #2.2 level 0.012 > volume #2.2 level 0.011 > volume #2.2 level 0.012 > show #!2.3 models > hide #!2.2 models > volume #2.3 level 0.012 > show #!2.4 models > hide #!2.3 models > volume #2.4 level 0.012 > show #!2.5 models > hide #!2.4 models > volume #2.5 level 0.012 > show #!2.6 models > hide #!2.5 models > volume #2.6 level 0.012 > volume #2.* level 0.012 > volume #4.* level 0.38 > volume #10.* level 0.011 > volume #12.* level 0.35 > volume #20.* level 0.17 > volume #23.* level 0.07 > volume color gray > windowsize size 500 500 Expected an integer >= 1 or a keyword > windowsize 500 500 > view matrix view matrix camera 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> clip list Using 2 clip planes: far offset 93.048, axis -0.908,0.281,-0.310, point 219.6,127.2,163) near offset -128.28, axis 0.908,-0.281,0.310, point 18.66,189.7,94.44) > ~clip > clip far 93.048 near -128.28 > save /Users/dalar193/wd/deltaRibosomes/EMDB_previews.cxs ——— End of log from Sun Sep 14 21:47:09 2025 ——— opened ChimeraX session > hide #!2.6 models > hide #!20.1 models > open > /Users/dalar193/wd/deltaRibosomes/aligned_maps_7k00scale/deltaE_HOMO_J230_APE_0.7Apix.mrc > id 20.1 name dE_J230_ape Opened dE_J230_ape as #7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.137, step 2, values float32 > open > /Users/dalar193/wd/deltaRibosomes/aligned_maps_7k00scale/deltaE_HOMO_J231_AP_0.7Apix.mrc > id 20.2 name dE_J231_ap Opened dE_J231_ap as #7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.132, step 2, values float32 > open > /Users/dalar193/wd/deltaRibosomes/aligned_maps_7k00scale/deltaE_HOMO_J232_PE_0.7Apix.mrc > id 20.3 name dE_J232_pe Opened dE_J232_pe as #7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.147, step 2, values float32 > open > /Users/dalar193/wd/deltaRibosomes/aligned_maps_7k00scale/deltaE_HOMO_J233_E_0.7Apix.mrc > id 20.4 name dE_J233_e Opened dE_J233_e as #7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.124, step 2, values float32 > open > /Users/dalar193/wd/deltaRibosomes/aligned_maps_7k00scale/deltaE_HOMO_J228_consensus_0.7Apix.mrc > id 20.5 name dE_J228_conc Opened dE_J228_conc as #7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.141, step 2, values float32 > hide #!20.5 models > hide #!20 models > show #!20 models > show #!20.1 models > volume step 1 > volume style surface > volume transparency 0 > volume color gray > volume unzone > windowsize 500 500 > view matrix camera > -0.21023,0.36217,-0.90809,-389.9,0.33485,0.89936,0.28116,316.33,0.91852,-0.24497,-0.31033,-45.092 > ~clip > clip far 93.048 near -128.28 > volume #2.* level 0.012 > volume #4.* level 0.38 > volume #10.* level 0.011 > volume #12.* level 0.35 > volume #20.* level 0.056 > volume #23.* level 0.07 > volume #23.3 level 0.065 > volume #20.* level 0.56 > volume #20.* level 0.7 > volume #20.* level 0.02 > volume #20.* level 0.07 > close #20.1-5 > open > /Users/dalar193/wd/deltaRibosomes/aligned_maps_7k00scale/deltaE_HOMO_J230_APE_0.7Apix.mrc > id 20.1 name dE_J230_ape Opened dE_J230_ape as #7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.137, step 2, values float32 > open > /Users/dalar193/wd/deltaRibosomes/aligned_maps_7k00scale/deltaE_HOMO_J231_AP_0.7Apix.mrc > id 20.2 name dE_J231_ap Opened dE_J231_ap as #7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.132, step 2, values float32 > open > /Users/dalar193/wd/deltaRibosomes/aligned_maps_7k00scale/deltaE_HOMO_J232_PE_0.7Apix.mrc > id 20.3 name dE_J232_pe Opened dE_J232_pe as #7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.147, step 2, values float32 > open > /Users/dalar193/wd/deltaRibosomes/aligned_maps_7k00scale/deltaE_HOMO_J233_E_0.7Apix.mrc > id 20.4 name dE_J233_e Opened dE_J233_e as #7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.124, step 2, values float32 > open > /Users/dalar193/wd/deltaRibosomes/aligned_maps_7k00scale/deltaE_HOMO_J228_consensus_0.7Apix.mrc > id 20.5 name dE_J228_conc Opened dE_J228_conc as #7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.141, step 2, values float32 > close #20.* > open > /Users/dalar193/wd/deltaRibosomes/aligned_maps_7k00scale/deltaE_HOMO_J230_APE_0.7Apix.mrc > id 20.1 name dE_J230_ape Opened dE_J230_ape as #7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.137, step 2, values float32 > open > /Users/dalar193/wd/deltaRibosomes/aligned_maps_7k00scale/deltaE_HOMO_J231_AP_0.7Apix.mrc > id 20.2 name dE_J231_ap Opened dE_J231_ap as #7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.132, step 2, values float32 > open > /Users/dalar193/wd/deltaRibosomes/aligned_maps_7k00scale/deltaE_HOMO_J232_PE_0.7Apix.mrc > id 20.3 name dE_J232_pe Opened dE_J232_pe as #7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.147, step 2, values float32 > open > /Users/dalar193/wd/deltaRibosomes/aligned_maps_7k00scale/deltaE_HOMO_J233_E_0.7Apix.mrc > id 20.4 name dE_J233_e Opened dE_J233_e as #7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.124, step 2, values float32 > open > /Users/dalar193/wd/deltaRibosomes/aligned_maps_7k00scale/deltaE_HOMO_J228_consensus_0.7Apix.mrc > id 20.5 name dE_J228_conc Opened dE_J228_conc as #7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.141, step 2, values float32 > volume #20.* level 0.056 > volume step 1 > volume style surface > volume transparency 0 > volume color gray > volume unzone > windowsize 500 500 > view matrix camera > -0.21023,0.36217,-0.90809,-389.9,0.33485,0.89936,0.28116,316.33,0.91852,-0.24497,-0.31033,-45.092 > ~clip > clip far 93.048 near -128.28 > volume color gray > hide #!20.5 models > hide #!20.4 models > hide #!20.3 models > hide #!20.2 models > hide #!20.1 models > show #!20.5 models > hide #!20.5 models > show #!20.5 models > save /Users/dalar193/Desktop/deltaRibosome_map_image_EMDB/dEJ228_conc.png > height 500 width 500 supersample 4 Directory ""/Users/dalar193/Desktop/deltaRibosome_map_image_EMDB"" does not exist > show #!20.5 models > save /Users/dalar193/Desktop/deltaRibosome_map_image_EMDB/dEJ228_conc.png > height 500 width 500 supersample 4 > hide #!20.5 models > show #!20.1 models > save /Users/dalar193/wd/deltaRibosomes/EMDB_previews.cxs ——— End of log from Sun Oct 12 20:03:57 2025 ——— opened ChimeraX session > open > /Users/dalar193/wd/deltaRibosomes/aligned_maps_7k00scale/delta9_refine3d_job169_consensus_0.7Apix.mrc > id 2.7 name d9_j169_conc Opened d9_j169_conc as #7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0267, step 2, values float32 > hide #!20.1 models > volume #2.7 step 1 > volume #2.7 step 1 level 0.015 > show #!20.5 models > hide #!20.5 models > show #!20.5 models > hide #!20.5 models > show #!20.5 models > hide #!20.5 models > volume #2.7 step 1 level 0.01 > show #!20.5 models > hide #!20.5 models > show #!20.5 models > hide #!20.5 models > show #!20.5 models > hide #!20.5 models > volume step 1 > volume style surface > volume transparency 0 > volume color gray > volume unzone > windowsize 500 500 > view matrix camera > -0.21023,0.36217,-0.90809,-389.9,0.33485,0.89936,0.28116,316.33,0.91852,-0.24497,-0.31033,-45.092 > ~clip > clip far 93.048 near -128.28 > hide #!2.7 models > show #!2.7 models > show #!20.5 models > hide #!2.7 models > show #!2.7 models > hide #!20.5 models > hide #!2.7 models > show #!4.1 models > hide #!4.1 models > show #!4.2 models > hide #!4.2 models > show #!4.2 models > show #!2.7 models > hide #!2.7 models > show #!2.7 models > hide #!2.7 models > show #!4.3 models > hide #!4.2 models > hide #!4.3 models > show #!4.4 models > hide #!4.4 models > show #!4.5 models > hide #!4.5 models > show #!4.6 models > volume #2.* level 0.012 > hide #!4.6 models > show #!2.7 models > show #!2.1 models > hide #!2.1 models > volume #2.* level 0.01 > hide #!2.7 models > show #!2.7 models > show #!20.5 models > hide #!2.7 models > show #!2.7 models > hide #!2.7 models > show #!2.7 models > volume #2.* level 0.012 > hide #!2.7 models > show #!2.7 models > hide #!20.5 models > show #!20.5 models > hide #!20.5 models > show #!20.5 models > hide #!20.5 models > show #!20.5 models > hide #!2.7 models > show #!2.6 models > hide #!2.6 models > show #!2.2 models > hide #!20.5 models > show #!20.5 models > hide #!20.5 models > show #!20.5 models > hide #!20.5 models > volume #2.* level 0.012 > volume #2.* level 0.01 > show #!20.5 models > hide #!20.5 models > show #!20.5 models > hide #!20.5 models > volume #2.* level 0.01 > volume #4.* level 0.38 > volume #10.* level 0.011 > volume #12.* level 0.35 > volume #20.* level 0.056 > volume #23.* level 0.07 > volume #23.3 level 0.065 > show #!12.1 models > hide #!2.2 models > hide #!12.1 models > show #!12.1 models > hide #!12.1 models > show #!12.1 models > show #!12.2 models > hide #!12.1 models > show #!12.3 models > hide #!12.2 models > show #!12.4 models > hide #!12.3 models > show #!12.5 models > hide #!12.4 models > show #!12.6 models > hide #!12.5 models > show #!12.7 models > hide #!12.6 models > show #!12.8 models > hide #!12.7 models > show #!12.9 models > hide #!12.8 models > show #!12.10 models > hide #!12.9 models > hide #!12.10 models > volume #23.3 level 0.065 > show #!2.7 models > save /Users/dalar193/Desktop/deltaRibosome_map_image_EMDB/d9j169_conc.png > height 500 width 500 supersample 4 > hide #!2.7 models > show #!4.10 models > save /Users/dalar193/Desktop/deltaRibosome_map_image_EMDB/d9J83_c0.png > height 500 width 500 supersample 4 > hide #!4.10 models > show #!4.1 models > save /Users/dalar193/Desktop/deltaRibosome_map_image_EMDB/d9J84_c1.png > height 500 width 500 supersample 4 > hide #!4.1 models > show #!4.2 models > save /Users/dalar193/Desktop/deltaRibosome_map_image_EMDB/d9J85_c2.png > height 500 width 500 supersample 4 > hide #!4.2 models > show #!4.3 models > save /Users/dalar193/Desktop/deltaRibosome_map_image_EMDB/d9J86_c3.png > height 500 width 500 supersample 4 > hide #!4.3 models > show #!4.4 models > save /Users/dalar193/Desktop/deltaRibosome_map_image_EMDB/d9J87_c4.png > height 500 width 500 supersample 4 > hide #!4.4 models > show #!4.5 models > save /Users/dalar193/Desktop/deltaRibosome_map_image_EMDB/d9J88_c5.png > height 500 width 500 supersample 4 > hide #!4.5 models > show #!4.6 models > save /Users/dalar193/Desktop/deltaRibosome_map_image_EMDB/d9J89_c6.png > height 500 width 500 supersample 4 > hide #!4.6 models > show #!4.7 models > save /Users/dalar193/Desktop/deltaRibosome_map_image_EMDB/d9J90_c7.png > height 500 width 500 supersample 4 > hide #!4.7 models > show #!4.8 models > save /Users/dalar193/Desktop/deltaRibosome_map_image_EMDB/d9J91_c8.png > height 500 width 500 supersample 4 > hide #!4.8 models > show #!4.9 models > save /Users/dalar193/Desktop/deltaRibosome_map_image_EMDB/d9J92_c9.png > height 500 width 500 supersample 4 > hide #!4.9 models > show #!10.4 models > save /Users/dalar193/Desktop/deltaRibosome_map_image_EMDB/d10j064_conc.png > height 500 width 500 supersample 4 > hide #!10.4 models > open > /Users/dalar193/wd/deltaRibosomes/aligned_maps_7k00scale/delta10_refine3d_job064_consensus_0.7Apix.mrc > id 10.4 name d10_j064_conc Opened d10_j064_conc as #7, grid size 391,421,391, pixel 0.7,0.7,0.7, shown at level 0.0248, step 2, values float32 > volume #10.* level 0.011 > volume step 1 > volume style surface > volume transparency 0 > volume color gray > hide #!10.4 models > show #!10.4 models > show #!2.7 models > hide #!2.7 models > show #!2.7 models > hide #!2.7 models > volume #10.4 level 0.010 > volume #10.* level 0.010 > show #!10.3 models > hide #!10.4 models > show #!10.2 models > hide #!10.3 models > show #!10.1 models > hide #!10.2 models > hide #!10.1 models > show #!10.4 models > save /Users/dalar193/Desktop/deltaRibosome_map_image_EMDB/d10j064_conc.png > height 500 width 500 supersample 4 > hide #!10.4 models > volume #10.* level 0.009 > show #!10.4 models > save /Users/dalar193/Desktop/deltaRibosome_map_image_EMDB/d10j064_conc.png > height 500 width 500 supersample 4 > hide #!10.4 models > show #!12.10 models > save /Users/dalar193/Desktop/deltaRibosome_map_image_EMDB/d10J53_c0.png > height 500 width 500 supersample 4 > hide #!12.10 models > show #!12.1 models > save /Users/dalar193/Desktop/deltaRibosome_map_image_EMDB/d10J54_c1.png > height 500 width 500 supersample 4 > hide #!12.1 models > show #!12.2 models > save /Users/dalar193/Desktop/deltaRibosome_map_image_EMDB/d10J55_c2.png > height 500 width 500 supersample 4 > hide #!12.2 models > show #!12.3 models > save /Users/dalar193/Desktop/deltaRibosome_map_image_EMDB/d10J56_c3.png > height 500 width 500 supersample 4 > hide #!12.3 models > show #!12.4 models > save /Users/dalar193/Desktop/deltaRibosome_map_image_EMDB/d10J57_c4.png > height 500 width 500 supersample 4 > hide #!12.4 models > show #!12.5 models > save /Users/dalar193/Desktop/deltaRibosome_map_image_EMDB/d10J58_c5.png > height 500 width 500 supersample 4 > hide #!12.5 models > show #!12.6 models > save /Users/dalar193/Desktop/deltaRibosome_map_image_EMDB/d10J59_c6.png > height 500 width 500 supersample 4 > hide #!12.6 models > show #!12.7 models > save /Users/dalar193/Desktop/deltaRibosome_map_image_EMDB/d10J60_c7.png > height 500 width 500 supersample 4 > hide #!12.7 models > show #!12.8 models > save /Users/dalar193/Desktop/deltaRibosome_map_image_EMDB/d10J61_c8.png > height 500 width 500 supersample 4 > hide #!12.8 models > show #!12.9 models > save /Users/dalar193/Desktop/deltaRibosome_map_image_EMDB/d10J62_c9.png > height 500 width 500 supersample 4 > hide #!12.9 models > save /Users/dalar193/wd/deltaRibosomes/EMDB_previews.cxs ——— End of log from Mon Oct 20 14:51:37 2025 ——— > view name session-start opened ChimeraX session > show #!1.2 models > view > open > /Users/dalar193/wd/deltaRibosomes/aligned_maps_7k00scale/8emm_LSQ-23S.pdb Summary of feedback from opening /Users/dalar193/wd/deltaRibosomes/aligned_maps_7k00scale/8emm_LSQ-23S.pdb --- warnings | PDB SEQRES record for chain B is incomplete. Ignoring input sequence records as basis for sequence. PDB SEQRES record for chain Y is incomplete. Ignoring input sequence records as basis for sequence. PDB SEQRES record for chain Z is incomplete. Ignoring input sequence records as basis for sequence. Chain information for 8emm_LSQ-23S.pdb #7 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available 3 | No description available 4 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available X | No description available Y Z | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available g | No description available h | No description available i | No description available j | No description available k | No description available l | No description available m | No description available n | No description available o | No description available p | No description available q | No description available r | No description available s | No description available t | No description available u | No description available v | No description available w | No description available x | No description available y | No description available z | No description available > style #!7#!1.2 stick Changed 291470 atom styles > hide #!7#!1.2 atoms > show #!7#!1.2 atoms > hide #!7#!1.2 cartoons > hide #!1.2 models > show #!1.2 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > open 8emm fromDatabase pdb format mmcif Summary of feedback from opening 8emm fetched from pdb --- note | Fetching compressed mmCIF 8emm from http://files.rcsb.org/download/8emm.cif 8emm title: Composite 70S ribosome structure for ""Atomistic simulations of the E. coli ribosome provide selection criteria for translationally active substrates [more info...] Chain information for 8emm #8 --- Chain | Description | UniProt 0 | 50S ribosomal protein L33 | F4NQ61_ECOLX 1-55 1 | 50S ribosomal protein L34 | RL34_ECO45 1-46 2 | 50S ribosomal protein L35 | RL35_ECOLI 1-65 3 | 50S ribosomal protein L36 | A0A0E2L017_ECOU3 1-38 4 | 50S ribosomal protein L31 | RL31_ECOLI 1-70 A | 16S rRNA | B | 30S ribosomal protein S2 | C3TPN2_ECOLX 1-241 C | 30S ribosomal protein S3 | RS3_ECO45 1-233 D | 30S ribosomal protein S4 | RS4_ECOLI 1-206 E | 30S ribosomal protein S5 | RS5_ECOLI 1-167 F | 30S ribosomal protein S6 | RS6_ECOLI 1-135 G | 30S ribosomal protein S7 | RS7_ECOLI 1-179 H | 30S ribosomal protein S8 | D7XKZ3_ECOLX 1-130 I | 30S ribosomal protein S9 | A0A1X3LT86_ECOLX 1-130 J | 30S ribosomal protein S10 | V0ANK5_ECOLX 1-103 K | 30S ribosomal protein S11 | A0A0H3PWX2_ECO5C 1-129 L | 30S ribosomal protein S12 | A0A0F1AUC4_9ENTR 1-124 M | 30S ribosomal protein S13 | A0A7U9IV78_ECOLX 1-118 N | 30S ribosomal protein S14 | U9Y6H3_ECOLX 1-101 O | 30S ribosomal protein S15 | D8EB41_ECOLX 1-89 P | 30S ribosomal protein S16 | C3SYP2_ECOLX 1-82 Q | 30S ribosomal protein S17 | A0A829A8C6_ECOLX 1-84 R | 30S ribosomal protein S18 | A0A0E2KXL3_ECOU3 1-75 S | 30S ribosomal protein S19 | S1EA57_ECOLX 1-92 T | 30S ribosomal protein S20 | C3TRH7_ECOLX 1-87 U | 30S ribosomal protein S21 | A0A0E2L2J1_ECOU3 1-71 X | mRNA | Y Z | Met-NH-tRNA | a | 23S rRNA | b | 5S rRNA | c | 50S ribosomal protein L2 | RL2_ECOLI 1-273 d | 50S ribosomal protein L3 | U9Y9G2_ECOLX 1-209 e | 50S ribosomal protein L4 | A0A7U9FY55_ECOLX 1-201 f | 50S ribosomal protein L5 | A0A829CFT8_ECOLX 1-179 g | 50S ribosomal protein L6 | A0A862ZNS7_ECOLX 1-177 h | 50S ribosomal protein L9 | V0YZK9_ECOLX 1-149 i | 50S ribosomal protein L13 | S1EW51_ECOLX 1-142 j | 50S ribosomal protein L14 | S1NW45_ECOLX 1-123 k | 50S ribosomal protein L15 | A0A037Y8L6_ECOLX 1-144 l | 50S ribosomal protein L16 | A0A7U9B8R8_ECOLX 1-136 m | 50S ribosomal protein L17 | A0A1X3LC97_ECOLX 1-127 n | 50S ribosomal protein L18 | E3PKY8_ECOH1 1-117 o | 50S ribosomal protein L19 | V0AJX1_ECOLX 1-115 p | 50S ribosomal protein L20 | RL20_ECO45 1-118 q | Ribosomal protein L21 | A0A829CSJ4_ECOLX 1-103 r | 50S ribosomal protein L22 | RL22_ECOLI 1-110 s | 50S ribosomal protein L23 | A0A829CFV1_ECOLX 1-100 t | 50S ribosomal protein L24 | A0A1X3KWX7_ECOLX 1-104 u | 50S ribosomal protein L25 | D7XH79_ECOLX 1-94 v | 50S ribosomal protein L27 | RL27_ECOLI 1-85 w | 50S ribosomal protein L28 | A0A1X3JA73_ECOLX 1-78 x | 50S ribosomal protein L29 | D6IEL0_ECOLX 1-63 y | 50S ribosomal protein L30 | V0YKA9_ECOLX 1-59 z | 50S ribosomal protein L32 | D7XI28_ECOLX 1-57 Non-standard residues in 8emm #8 --- K — potassium ion MET — methionine MG — magnesium ion MS6 — (2S)-2-amino-4-(methylsulfanyl)butane-1-thiol PAR — paromomycin (paromomycin I; amminosidin; catenulin; crestomycin; monomycin A; neomycin E) SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34)) SPM — spermine ZN — zinc ion > style #!7-8#!1.2 stick Changed 437205 atom styles > mmaker #8/a to #1.2/a Using Nucleic matrix instead of BLOSUM-62 for matching Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 8emm, chain a (#1.2) with 8emm, chain a (#8), sequence alignment score = 10743.2 RMSD between 2753 pruned atom pairs is 0.268 angstroms; (across all 2753 pairs: 0.268) > hide #1.2 target ac > color #1.2 white > color #1.2/a:2057-2065 #7EAAEE > color #1.2/a:2445-2454 #EDD670 > color #1.2/a:2499-2508 light green > color #1.2/a:2580-2588 light salmon > color #1.2/a:2606-2611 #B49BE6 > show #1.2/a:2057-2065,2445-2454,2499-2508,2580-2588,2606-2611 target ac > nucleotides tube/slab > nucleotides :H2U fill > hide #!8 models > hide #!7 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > view > lighting gentle > cartoon suppressBackboneDisplay true Computing secondary structure > show #1.2/a:2057-2065,2445-2454,2499-2508,2580-2588,2606-2611 target ac > hide #1.2 target ac > show #1.2/a:2057-2065,2445-2454,2499-2508,2580-2588,2606-2611 target ac > cartoon suppressBackboneDisplay true > show #1.2/a:2057-2065,2445-2454,2499-2508,2580-2588,2606-2611 target ac [Repeated 1 time(s)] > hide #1.2 > show #1.2/a:2057-2065,2445-2454,2499-2508,2580-2588,2606-2611 target ac > hide #1.2 > show #1.2/a:2057-2065,2445-2454,2499-2508,2580-2588,2606-2611 target ac > hide #1.2 target ac > show #1.2/a:2057-2065,2445-2454,2499-2508,2580-2588,2606-2611 target ac > cartoon suppressBackboneDisplay false > hide #1.2 target ac > show #1.2/a:2057-2065,2445-2454,2499-2508,2580-2588,2606-2611 target ac > cartoon suppressBackboneDisplay false > hide #1.2 target ac > show #1.2/a:2057-2065,2445-2454,2499-2508,2580-2588,2606-2611 target ac > hide #1.2 target ac > show #1.2/b:30-50 target ac > view > hide #1.2 target ac > show #1.2/c:30-50 target ac > view > lighting simple > cartoon suppressBackboneDisplay true OpenGL version: 4.1 Metal - 83.1 OpenGL renderer: Apple M2 Pro OpenGL vendor: Apple Python: 3.11.9 Locale: UTF-8 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,9 Model Number: Z17G002M2KS/A Chip: Apple M2 Pro Total Number of Cores: 10 (6 performance and 4 efficiency) Memory: 32 GB System Firmware Version: 11881.140.96 OS Loader Version: 8422.141.2.700.1 Software: System Software Overview: System Version: macOS 13.7.8 (22H730) Kernel Version: Darwin 22.6.0 Time since boot: 41 days, 35 minutes Graphics/Displays: Apple M2 Pro: Chipset Model: Apple M2 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: EA275UHD: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 3840 x 2160 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported EA244WMi: Resolution: 1200 x 1920 UI Looks like: 1200 x 1920 @ 60.00Hz Mirror: Off Online: Yes Rotation: 90 Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.1 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 25.4.0 babel: 2.17.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 3.12.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.4 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.1.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.61.4 ChimeraX-AtomicLibrary: 14.2.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.0 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.11.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 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: 1.4.1 ChimeraX-Hbonds: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.7.3 ChimeraX-Label: 1.2 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.2 ChimeraX-Map: 1.3 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: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.1.0 ChimeraX-MDcrds: 2.17.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.6 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: 1.0.1 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.15.2 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.12 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.4.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.5 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.10 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.3 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.49.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.5.2 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: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.3.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.4 debugpy: 1.8.19 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.61.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.15.1 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.11 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.3.0 ipykernel: 6.30.1 ipython: 9.5.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.8 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.6.3 jupyter_core: 5.9.1 jupyterlab_widgets: 3.0.16 kiwisolver: 1.4.9 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.1 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.0 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.5 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.5.1 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.12.5 pydantic-settings: 2.12.0 pydantic_core: 2.41.5 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.6 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.9.1 PyQt6-Qt6: 6.9.2 PyQt6-WebEngine-commercial: 6.9.0 PyQt6-WebEngine-Qt6: 6.9.2 PyQt6_sip: 13.10.2 pytest: 9.0.2 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.1 python-multipart: 0.0.21 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.1.0 roman-numerals-py: 4.1.0 rpds-py: 0.30.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8.3 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.2.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 sse-starlette: 3.2.0 stack-data: 0.6.3 starlette: 0.52.1 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.4 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 urllib3: 2.6.3 uvicorn: 0.40.0 wcwidth: 0.3.2 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 yarl: 1.22.0 }}} " defect closed normal Depiction not a bug Elaine Meng all ChimeraX