Opened 9 months ago
Last modified 9 months ago
#16704 assigned defect
ISOLDE: Unparameterised residue detected
Reported by: | Owned by: | Tristan Croll | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Third Party | Version: | |
Keywords: | Cc: | Greg Couch | |
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Windows-10-10.0.19045 ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Replace this text with list of actions that caused this problem to occur Log: UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open "C:\Users\jlerath\Desktop\Ec24 > CryoEM\P49_Ec24_7b5k_fitting_20250127.cxs" format session Opened cryosparc_P49_J120_004_volume_map_sharp.mrc as #1.1, grid size 448,448,448, pixel 1.18, shown at level 0.66, step 1, values float32 Opened cryosparc_P49_J119_004_volume_map_sharp.mrc as #1.2, grid size 448,448,448, pixel 1.18, shown at level 0.875, step 1, values float32 Opened cryosparc_P49_J118_003_volume_map_sharp.mrc as #1.3, grid size 448,448,448, pixel 1.18, shown at level 0.849, step 1, values float32 Opened cryosparc_P49_J117_004_volume_map_sharp.mrc as #1.4, grid size 448,448,448, pixel 1.18, shown at level 0.628, step 1, values float32 Opened J117_004_volume_map_deepEMhancer.mrc as #2, grid size 448,448,448, pixel 1.18, shown at level 0.1, step 1, values float32 Log from Mon Jan 27 14:19:42 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open "C:/Users/jlerath/Desktop/Ec24 > CryoEM/Ec24_P49_MaskMakingSessionv2_2020123.cxs" Opened cryosparc_P49_J91_006_volume_map_sharp.mrc as #47, grid size 448,448,448, pixel 1.18, shown at level 1, step 1, values float32 Opened cryosparc_P49_J92_006_volume_map_sharp.mrc as #48, grid size 448,448,448, pixel 1.18, shown at level 0.796, step 1, values float32 Opened cryosparc_P49_J95_007_volume_map_sharp.mrc as #49, grid size 448,448,448, pixel 1.18, shown at level 0.69, step 1, values float32 Opened cryosparc_P49_J96_006_volume_map_sharp.mrc as #50, grid size 448,448,448, pixel 1.18, shown at level 0.726, step 1, values float32 Opened cryosparc_P49_J94_007_volume_map_sharp.mrc as #51, grid size 448,448,448, pixel 1.18, shown at level 0.455, step 1, values float32 Opened cryosparc_P49_J91_006_volume_map_sharp.mrc gaussian as #1, grid size 448,448,448, pixel 1.18, shown at level 0.0993, step 1, values float32 Opened cryosparc_P49_J91_50SMasked_20250123.mrc as #6, grid size 448,448,448, pixel 1.18, shown at level 0.5, step 1, values float32 Opened cryosparc_P49_J91_30SMasked_20250123.mrc as #7, grid size 448,448,448, pixel 1.18, shown at level 0.5, step 1, values float32 Opened cryosparc_P49_J91_APEMasked_20250123.mrc as #8, grid size 448,448,448, pixel 1.18, shown at level 0.5, step 1, values float32 Opened cryosparc_P49_J91_50SMask_20250123.mrc as #9, grid size 448,448,448, pixel 1.18, shown at level 0.105, step 1, values float32 Opened cryosparc_P49_J91_30SMask_20250123.mrc as #3, grid size 448,448,448, pixel 1.18, shown at level 0.105, step 1, values float32 Opened cryosparc_P49_J91_APEMask_20250123.mrc as #10, grid size 448,448,448, pixel 1.18, shown at level 0.105, step 1, values float32 Opened cryosparc_P49_J91_30SAPEMask_20250123.mrc as #4, grid size 448,448,448, pixel 1.18, shown at level 0.105, step 1, values float32 Opened volume maximum as #5, grid size 448,448,448, pixel 1.18, shown at level 0.105, step 1, values float32 Log from Thu Jan 23 17:30:05 2025 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa11684.3421.rartemp/J83_class_00_00008_volume.mrc Opened J83_class_00_00008_volume.mrc as #1, grid size 192,192,192, pixel 2.76, shown at level 2.49, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa11684.3421.rartemp/J83_class_01_00008_volume.mrc Opened J83_class_01_00008_volume.mrc as #2, grid size 192,192,192, pixel 2.76, shown at level 2.22, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa11684.3421.rartemp/J83_class_02_00008_volume.mrc Opened J83_class_02_00008_volume.mrc as #3, grid size 192,192,192, pixel 2.76, shown at level 2.22, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa11684.3421.rartemp/J83_class_03_00008_volume.mrc Opened J83_class_03_00008_volume.mrc as #4, grid size 192,192,192, pixel 2.76, shown at level 2.4, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa11684.3421.rartemp/J83_class_04_00008_volume.mrc Opened J83_class_04_00008_volume.mrc as #5, grid size 192,192,192, pixel 2.76, shown at level 2.35, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa20644.4920.rartemp/J84_class_00_00051_volume.mrc Opened J84_class_00_00051_volume.mrc as #6, grid size 192,192,192, pixel 2.76, shown at level 1.92, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa20644.4920.rartemp/J84_class_01_00051_volume.mrc Opened J84_class_01_00051_volume.mrc as #7, grid size 192,192,192, pixel 2.76, shown at level 2.54, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa20644.4920.rartemp/J84_class_02_00051_volume.mrc Opened J84_class_02_00051_volume.mrc as #8, grid size 192,192,192, pixel 2.76, shown at level 2.56, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa20644.4920.rartemp/J84_class_03_00051_volume.mrc Opened J84_class_03_00051_volume.mrc as #9, grid size 192,192,192, pixel 2.76, shown at level 2.86, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa20644.4920.rartemp/J84_class_04_00051_volume.mrc Opened J84_class_04_00051_volume.mrc as #10, grid size 192,192,192, pixel 2.76, shown at level 2.85, step 1, values float32 > close #1-10 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa17180.7075.rartemp/J82_class_00_00069_volume.mrc Opened J82_class_00_00069_volume.mrc as #1, grid size 192,192,192, pixel 2.76, shown at level 1.97, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa17180.7075.rartemp/J82_class_01_00069_volume.mrc Opened J82_class_01_00069_volume.mrc as #2, grid size 192,192,192, pixel 2.76, shown at level 1.99, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa17180.7075.rartemp/J82_class_02_00069_volume.mrc Opened J82_class_02_00069_volume.mrc as #3, grid size 192,192,192, pixel 2.76, shown at level 2.08, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa17180.7075.rartemp/J82_class_03_00069_volume.mrc Opened J82_class_03_00069_volume.mrc as #4, grid size 192,192,192, pixel 2.76, shown at level 2.08, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa17180.7075.rartemp/J82_class_04_00069_volume.mrc Opened J82_class_04_00069_volume.mrc as #5, grid size 192,192,192, pixel 2.76, shown at level 2.3, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa2592.8618.rartemp/J83_class_00_00008_volume.mrc Opened J83_class_00_00008_volume.mrc as #6, grid size 192,192,192, pixel 2.76, shown at level 2.49, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa2592.8618.rartemp/J83_class_01_00008_volume.mrc Opened J83_class_01_00008_volume.mrc as #7, grid size 192,192,192, pixel 2.76, shown at level 2.22, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa2592.8618.rartemp/J83_class_02_00008_volume.mrc Opened J83_class_02_00008_volume.mrc as #8, grid size 192,192,192, pixel 2.76, shown at level 2.22, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa2592.8618.rartemp/J83_class_03_00008_volume.mrc Opened J83_class_03_00008_volume.mrc as #9, grid size 192,192,192, pixel 2.76, shown at level 2.4, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa2592.8618.rartemp/J83_class_04_00008_volume.mrc Opened J83_class_04_00008_volume.mrc as #10, grid size 192,192,192, pixel 2.76, shown at level 2.35, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa20644.9547.rartemp/J84_class_00_00051_volume.mrc Opened J84_class_00_00051_volume.mrc as #11, grid size 192,192,192, pixel 2.76, shown at level 1.92, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa20644.9547.rartemp/J84_class_01_00051_volume.mrc Opened J84_class_01_00051_volume.mrc as #12, grid size 192,192,192, pixel 2.76, shown at level 2.54, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa20644.9547.rartemp/J84_class_02_00051_volume.mrc Opened J84_class_02_00051_volume.mrc as #13, grid size 192,192,192, pixel 2.76, shown at level 2.56, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa20644.9547.rartemp/J84_class_03_00051_volume.mrc Opened J84_class_03_00051_volume.mrc as #14, grid size 192,192,192, pixel 2.76, shown at level 2.86, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa20644.9547.rartemp/J84_class_04_00051_volume.mrc Opened J84_class_04_00051_volume.mrc as #15, grid size 192,192,192, pixel 2.76, shown at level 2.85, step 1, values float32 > hide #!15 models > hide #!14 models > hide #!13 models > hide #!12 models > hide #!11 models > hide #!10 models > hide #!9 models > hide #!8 models > hide #!7 models > hide #!6 models > volume #1 level 0.6907 > volume #2 level 0.8884 > volume #1 level 0.75 > volume #2 level 0.75 > volume #3 level 0.75 > volume #4 level 0.75 > volume #5 level 0.75 > hide #!5 models > hide #!4 models > hide #!3 models > hide #!2 models > show #!2 models > hide #!1 models > hide #!2 models > show #!3 models > lighting soft > show #!2 models > hide #!3 models > hide #!2 models > show #!4 models > set bgColor white > volume #4 level 0.631 > show #!2 models > volume #3 level 0.6292 > volume #2 level 0.5261 > volume #1 level 0.4643 > hide #!4 models > hide #!3 models > hide #!2 models > show #!2 models > hide #!1 models > hide #!2 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!6 models > volume #6 level 1.088 > volume #7 level 0.9574 > volume #8 level 1.008 > volume #9 level 1.051 > volume #10 level 0.9908 > hide #!10 models > hide #!9 models > hide #!8 models > hide #!7 models > show #!9 models > hide #!6 models > show #!6 models > show #!1 models > show #!3 models > show #!5 models > hide #!3 models > hide #!1 models > hide #!5 models > hide #!6 models > hide #!9 models > show #!2 models > show #!4 models > show #!7 models > show #!8 models > show #!10 models > hide #!10 models > hide #!8 models > hide #!7 models > hide #!4 models > hide #!2 models > show #!11 models > volume #11 level 0.4083 > hide #!11 models > show #!12 models > volume #12 level 1.385 > show #!13 models > show #!14 models > show #!15 models > close #12-15 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa4604.14277.rartemp/J86_class_00_00028_volume.mrc Opened J86_class_00_00028_volume.mrc as #12, grid size 192,192,192, pixel 2.76, shown at level 1.99, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa4604.14277.rartemp/J86_class_01_00028_volume.mrc Opened J86_class_01_00028_volume.mrc as #13, grid size 192,192,192, pixel 2.76, shown at level 2.24, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa4604.14277.rartemp/J86_class_02_00028_volume.mrc Opened J86_class_02_00028_volume.mrc as #14, grid size 192,192,192, pixel 2.76, shown at level 2.28, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa4604.14277.rartemp/J86_class_03_00028_volume.mrc Opened J86_class_03_00028_volume.mrc as #15, grid size 192,192,192, pixel 2.76, shown at level 2.52, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa4604.14277.rartemp/J86_class_04_00028_volume.mrc Opened J86_class_04_00028_volume.mrc as #16, grid size 192,192,192, pixel 2.76, shown at level 2.55, step 1, values float32 > volume #16 level 1.236 > volume #15 level 0.9991 > volume #14 level 0.9905 > volume #13 level 1.031 > volume #12 level 0.4628 > hide #!16 models > hide #!15 models > hide #!14 models > hide #!13 models > volume #12 level 0.4076 > show #!13 models > hide #!12 models > volume #13 level 0.9049 > show #!14 models > show #!15 models > show #!16 models > hide #!16 models > hide #!15 models > hide #!14 models > hide #!13 models > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa15404.28948.rartemp/J85_class_00_00039_volume.mrc Opened J85_class_00_00039_volume.mrc as #17, grid size 192,192,192, pixel 2.76, shown at level 1.97, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa15404.28948.rartemp/J85_class_01_00039_volume.mrc Opened J85_class_01_00039_volume.mrc as #18, grid size 192,192,192, pixel 2.76, shown at level 2.07, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa15404.28948.rartemp/J85_class_02_00039_volume.mrc Opened J85_class_02_00039_volume.mrc as #19, grid size 192,192,192, pixel 2.76, shown at level 2.22, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa15404.28948.rartemp/J85_class_03_00039_volume.mrc Opened J85_class_03_00039_volume.mrc as #20, grid size 192,192,192, pixel 2.76, shown at level 2.46, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa15404.28948.rartemp/J85_class_04_00039_volume.mrc Opened J85_class_04_00039_volume.mrc as #21, grid size 192,192,192, pixel 2.76, shown at level 2.54, step 1, values float32 > volume #21 level 1.145 > volume #20 level 1.077 > volume #19 level 1.117 > volume #18 level 0.9265 > volume #17 level 0.5945 > hide #!21 models > hide #!20 models > hide #!19 models > hide #!18 models > hide #!17 models > show #!18 models > show #!17 models > hide #!18 models > hide #!17 models > show #!19 models > volume #19 level 0.7987 > volume #18 level 0.6502 > volume #17 level 0.4033 > hide #!18 models > hide #!17 models > show #!17 models > hide #!19 models > show #!18 models > hide #!17 models > hide #!18 models > show #!19 models > hide #!19 models > show #!20 models > volume #20 level 0.8199 > show #!19 models > hide #!19 models > show #!1 models > hide #!1 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!17 models > hide #!17 models > show #!18 models > hide #!18 models > show #!19 models > hide #!19 models > show #!19 models > hide #!20 models > hide #!19 models > show #!21 models > show #!20 models > show #!11 models > hide #!20 models > hide #!21 models > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa20860.42981.rartemp/J78_class_00_00042_volume.mrc Opened J78_class_00_00042_volume.mrc as #22, grid size 192,192,192, pixel 2.76, shown at level 2, step 1, values float32 > volume #22 level 0.4653 > hide #!22 models > show #!22 models > hide #!22 models > show #!22 models > hide #!22 models > show #!22 models > hide #!22 models > show #!22 models > close #22 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa3848.34654.rartemp/J89_class_00_00008_volume.mrc Opened J89_class_00_00008_volume.mrc as #22, grid size 192,192,192, pixel 2.76, shown at level 2.57, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa3848.34654.rartemp/J89_class_01_00008_volume.mrc Opened J89_class_01_00008_volume.mrc as #23, grid size 192,192,192, pixel 2.76, shown at level 2.5, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa3848.34654.rartemp/J89_class_02_00008_volume.mrc Opened J89_class_02_00008_volume.mrc as #24, grid size 192,192,192, pixel 2.76, shown at level 2.5, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa3848.34654.rartemp/J89_class_03_00008_volume.mrc Opened J89_class_03_00008_volume.mrc as #25, grid size 192,192,192, pixel 2.76, shown at level 2.45, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa3848.34654.rartemp/J89_class_04_00008_volume.mrc Opened J89_class_04_00008_volume.mrc as #26, grid size 192,192,192, pixel 2.76, shown at level 2.42, step 1, values float32 > hide #!11 models > volume #26 level 1.033 > volume #25 level 1.031 > volume #24 level 0.9924 > volume #23 level 1.043 > volume #22 level 0.9823 > hide #!26 models > hide #!25 models > hide #!24 models > hide #!23 models > show #!23 models > show #!24 models > show #!25 models > show #!26 models > hide #!26 models > hide #!25 models > hide #!24 models > hide #!22 models > hide #!23 models > show #!24 models > hide #!24 models > show #!25 models > volume #25 level 0.9333 > volume #25 level 0.738 > hide #!25 models > show #!26 models > volume #26 level 0.721 > show #!24 models > hide #!24 models > show #!22 models > hide #!22 models > show #!25 models > show #!24 models > show #!23 models > show #!22 models > hide #!22 models > hide #!23 models > hide #!24 models > hide #!25 models > hide #!26 models > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa30360.28844.rartemp/J87_class_00_00043_volume.mrc Opened J87_class_00_00043_volume.mrc as #27, grid size 192,192,192, pixel 2.76, shown at level 1.97, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa30360.28844.rartemp/J87_class_01_00043_volume.mrc Opened J87_class_01_00043_volume.mrc as #28, grid size 192,192,192, pixel 2.76, shown at level 2.04, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa30360.28844.rartemp/J87_class_02_00043_volume.mrc Opened J87_class_02_00043_volume.mrc as #29, grid size 192,192,192, pixel 2.76, shown at level 2.08, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa30360.28844.rartemp/J87_class_03_00043_volume.mrc Opened J87_class_03_00043_volume.mrc as #30, grid size 192,192,192, pixel 2.76, shown at level 2.26, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa30360.28844.rartemp/J87_class_04_00043_volume.mrc Opened J87_class_04_00043_volume.mrc as #31, grid size 192,192,192, pixel 2.76, shown at level 2.91, step 1, values float32 > volume #31 level 1.669 > volume #30 level 0.9108 > volume #29 level 0.7639 > volume #28 level 0.6371 > volume #27 level 0.5095 > hide #!31 models > hide #!30 models > hide #!29 models > hide #!28 models > show #!28 models > hide #!27 models > show #!29 models > hide #!28 models > show #!30 models > hide #!29 models > show #!31 models > hide #!30 models > show #!30 models > show #!29 models > show #!28 models > show #!27 models > hide #!31 models > hide #!30 models > hide #!29 models > hide #!28 models > hide #!27 models > show #!27 models > show #!28 models > show #!29 models > show #!30 models > show #!31 models > surface dust #27 size 27.6 > surface dust #28 size 27.6 > surface dust #29 size 27.6 > surface dust #30 size 27.6 > surface dust #31 size 27.6 > surface dust #27-31 size 0 > show #!22 models > hide #!22 models > show #!22 models > show #!23 models > show #!24 models > show #!25 models > show #!26 models > hide #!25 models > hide #!26 models > hide #!27 models > hide #!28 models > hide #!29 models > hide #!30 models > hide #!31 models > hide #!22 models > hide #!23 models > hide #!24 models > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa2040.15642.rartemp/J88_class_00_00006_volume.mrc Opened J88_class_00_00006_volume.mrc as #32, grid size 192,192,192, pixel 2.76, shown at level 2.31, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa2040.15642.rartemp/J88_class_01_00006_volume.mrc Opened J88_class_01_00006_volume.mrc as #33, grid size 192,192,192, pixel 2.76, shown at level 2.32, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa2040.15642.rartemp/J88_class_02_00006_volume.mrc Opened J88_class_02_00006_volume.mrc as #34, grid size 192,192,192, pixel 2.76, shown at level 2.3, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa2040.15642.rartemp/J88_class_03_00006_volume.mrc Opened J88_class_03_00006_volume.mrc as #35, grid size 192,192,192, pixel 2.76, shown at level 2.36, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa2040.15642.rartemp/J88_class_04_00006_volume.mrc Opened J88_class_04_00006_volume.mrc as #36, grid size 192,192,192, pixel 2.76, shown at level 2.31, step 1, values float32 > hide #!36 models > hide #!35 models > hide #!34 models > hide #!33 models > hide #!32 models > show #!32 models > volume #32 level 1.092 > show #!33 models > hide #!32 models > volume #33 level 1.019 > show #!34 models > hide #!33 models > volume #34 level 0.9697 > hide #!34 models > show #!35 models > volume #35 level 1.141 > hide #!35 models > show #!36 models > volume #36 level 1.057 > show #!35 models > show #!34 models > show #!33 models > show #!32 models > surface dust #32 size 27.6 > surface dust #33 size 27.6 > surface dust #34 size 27.6 > surface dust #35 size 27.6 > surface dust #36 size 27.6 > surface dust #32-36 size 0 > hide #!36 models > hide #!35 models > hide #!34 models > hide #!33 models > show #!33 models > hide #!32 models > show #!32 models > hide #!32 models > show #!34 models > hide #!33 models > show #!33 models > hide #!33 models > hide #!34 models > show #!35 models > hide #!35 models > show #!36 models > hide #!36 models > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa28564.29871.rartemp/J74_class_00_00146_volume.mrc Opened J74_class_00_00146_volume.mrc as #37, grid size 192,192,192, pixel 2.76, shown at level 1.96, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa28564.29871.rartemp/J74_class_01_00146_volume.mrc Opened J74_class_01_00146_volume.mrc as #38, grid size 192,192,192, pixel 2.76, shown at level 1.98, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa28564.29871.rartemp/J74_class_02_00146_volume.mrc Opened J74_class_02_00146_volume.mrc as #39, grid size 192,192,192, pixel 2.76, shown at level 1.98, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa28564.29871.rartemp/J74_class_03_00146_volume.mrc Opened J74_class_03_00146_volume.mrc as #40, grid size 192,192,192, pixel 2.76, shown at level 2.12, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa28564.29871.rartemp/J74_class_04_00146_volume.mrc Opened J74_class_04_00146_volume.mrc as #41, grid size 192,192,192, pixel 2.76, shown at level 2.66, step 1, values float32 > volume #41 level 1.593 > volume #40 level 0.7917 > volume #39 level 0.4303 > volume #38 level 0.2986 > volume #37 level 0.3572 > hide #!41 models > hide #!40 models > hide #!39 models > hide #!38 models > hide #!37 models > show #!37 models > show #!38 models > hide #!37 models > hide #!38 models > show #!39 models > show #!37 models > hide #!39 models > show #!39 models > hide #!37 models > show #!37 models > hide #!37 models > show #!37 models > hide #!37 models > show #!37 models > hide #!39 models > show #!39 models > hide #!39 models > show #!39 models > hide #!39 models > hide #!37 models > show #!40 models > show #!41 models > hide #!40 models > hide #!41 models > show #!37 models > show #!39 models > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa16576.42575.rartemp/J75_class_00_00090_volume.mrc Opened J75_class_00_00090_volume.mrc as #42, grid size 192,192,192, pixel 2.76, shown at level 1.95, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa16576.42575.rartemp/J75_class_01_00090_volume.mrc Opened J75_class_01_00090_volume.mrc as #43, grid size 192,192,192, pixel 2.76, shown at level 1.95, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa16576.42575.rartemp/J75_class_02_00090_volume.mrc Opened J75_class_02_00090_volume.mrc as #44, grid size 192,192,192, pixel 2.76, shown at level 2.22, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa16576.42575.rartemp/J75_class_03_00090_volume.mrc Opened J75_class_03_00090_volume.mrc as #45, grid size 192,192,192, pixel 2.76, shown at level 2.28, step 1, values float32 > open > C:/Users/jlerath/AppData/Local/Temp/Rar$DRa16576.42575.rartemp/J75_class_04_00090_volume.mrc Opened J75_class_04_00090_volume.mrc as #46, grid size 192,192,192, pixel 2.76, shown at level 2.38, step 1, values float32 > hide #!37 models > hide #!39 models > volume #46 level 1.296 > volume #42 level 0.4477 > volume #43 level 0.44 > volume #44 level 1.039 > volume #45 level 1.043 > volume #46 level 0.9303 > hide #!43 models > hide #!44 models > hide #!45 models > hide #!46 models > show #!43 models > hide #!42 models > hide #!43 models > show #!45 models > show #!44 models > show #!43 models > hide #!43 models > hide #!45 models > show #!46 models > hide #!44 models > show #!42 models > hide #!46 models > show #!45 models > show #!44 models > show #!46 models > hide #!45 models > hide #!44 models > hide #!42 models > hide #!46 models > show #!44 models > volume #44 level 0.8706 > show #!45 models > volume #45 level 0.9528 > show #!43 models > hide #!44 models > hide #!45 models > show #!44 models > hide #!43 models > hide #!44 models > open C:/Users/jlerath/Downloads/cryosparc_P49_J92_006_volume_map_sharp.mrc Opened cryosparc_P49_J92_006_volume_map_sharp.mrc as #47, grid size 448,448,448, pixel 1.18, shown at level 0.796, step 2, values float32 > open C:/Users/jlerath/Downloads/cryosparc_P49_J93_006_volume_map_sharp.mrc Opened cryosparc_P49_J93_006_volume_map_sharp.mrc as #48, grid size 448,448,448, pixel 1.18, shown at level 0.883, step 2, values float32 > open C:/Users/jlerath/Downloads/cryosparc_P49_J91_006_volume_map_sharp.mrc Opened cryosparc_P49_J91_006_volume_map_sharp.mrc as #49, grid size 448,448,448, pixel 1.18, shown at level 0.901, step 2, values float32 > open C:/Users/jlerath/Downloads/cryosparc_P49_J94_007_volume_map_sharp.mrc Opened cryosparc_P49_J94_007_volume_map_sharp.mrc as #50, grid size 448,448,448, pixel 1.18, shown at level 0.455, step 2, values float32 > volume #47-50 step 1 > hide #!50 models > hide #!49 models > hide #!48 models > surface dust #47 size 11.8 > surface dust #47 size 5 > volume #47 level 0.5 > surface dust #47 size 15 > show #!48 models > hide #!47 models > surface dust #48 size 5 > show #!47 models > hide #!47 models > show #!49 models > hide #!48 models > surface dust #49 size 5 > show #!48 models > color #48 #aaaaffff models > hide #!48 models > show #!48 models > volume #49 level 0.883 > hide #!48 models > show #!48 models > hide #!49 models > show #!49 models > hide #!49 models > show #!49 models > hide #!48 models > show #!48 models > hide #!48 models > show #!48 models > close #48 > hide #!49 models > show #!50 models > volume #50 level 0.35 > surface dust #50 size 5 > show #!47 models > hide #!50 models > volume #47 level 0.75 > volume #47 level 1 > volume #47 level 1.2 > volume #47 level 0.5 > open C:/Users/jlerath/Downloads/cryosparc_P49_J95_007_volume_map_sharp.mrc Opened cryosparc_P49_J95_007_volume_map_sharp.mrc as #48, grid size 448,448,448, pixel 1.18, shown at level 0.69, step 2, values float32 > open C:/Users/jlerath/Downloads/cryosparc_P49_J96_006_volume_map_sharp.mrc Opened cryosparc_P49_J96_006_volume_map_sharp.mrc as #51, grid size 448,448,448, pixel 1.18, shown at level 0.726, step 2, values float32 > volume #48,51 step 1 > hide #!47 models > hide #!48 models > show #!48 models > surface dust #48,51 size 5 > hide #!48 models > show #!48 models > hide #!51 models > show #!51 models > hide #!51 models > show #!51 models > hide #!51 models > show #!51 models > hide #!51 models > hide #!48 models > show #!48 models > show #!49 models > hide #!48 models > show #!47 models > hide #!49 models > show #!49 models > hide #!47 models > show #!47 models > volume #47 level 1 > volume #49 level 1 > hide #!49 models > show #!49 models > hide #!49 models > show #!49 models > hide #!49 models > show #!49 models > hide #!49 models > show #!49 models > close #47-51 > open C:/Users/jlerath/Downloads/cryosparc_P49_J91_006_volume_map_sharp.mrc Opened cryosparc_P49_J91_006_volume_map_sharp.mrc as #47, grid size 448,448,448, pixel 1.18, shown at level 0.901, step 2, values float32 > open C:/Users/jlerath/Downloads/cryosparc_P49_J92_006_volume_map_sharp.mrc Opened cryosparc_P49_J92_006_volume_map_sharp.mrc as #48, grid size 448,448,448, pixel 1.18, shown at level 0.796, step 2, values float32 > open C:/Users/jlerath/Downloads/cryosparc_P49_J95_007_volume_map_sharp.mrc Opened cryosparc_P49_J95_007_volume_map_sharp.mrc as #49, grid size 448,448,448, pixel 1.18, shown at level 0.69, step 2, values float32 > open C:/Users/jlerath/Downloads/cryosparc_P49_J96_006_volume_map_sharp.mrc Opened cryosparc_P49_J96_006_volume_map_sharp.mrc as #50, grid size 448,448,448, pixel 1.18, shown at level 0.726, step 2, values float32 > open C:/Users/jlerath/Downloads/cryosparc_P49_J94_007_volume_map_sharp.mrc Opened cryosparc_P49_J94_007_volume_map_sharp.mrc as #51, grid size 448,448,448, pixel 1.18, shown at level 0.455, step 2, values float32 > volume #47-51 step 1 > surface dust #47-51 size 4 > surface dust #47-51 size 5 > hide #!51 models > hide #!50 models > hide #!49 models > hide #!48 models > volume #47 level 1 > open "C:/Users/jlerath/Desktop/Legionella CryoEM/Published > Structures/7b5k/7b5k-pdb-bundle1.pdb" "C:/Users/jlerath/Desktop/Legionella > CryoEM/Published Structures/7b5k/7b5k-pdb-bundle2.pdb" Summary of feedback from opening C:/Users/jlerath/Desktop/Legionella CryoEM/Published Structures/7b5k/7b5k-pdb-bundle1.pdb --- warning | Ignored bad PDB record found on line 1 HEADER RIBOSOME 2020-12-03 XXXX Summary of feedback from opening C:/Users/jlerath/Desktop/Legionella CryoEM/Published Structures/7b5k/7b5k-pdb-bundle2.pdb --- warning | Ignored bad PDB record found on line 1 HEADER RIBOSOME 2020-12-03 XXXX Chain information for 7b5k-pdb-bundle1.pdb #52 --- 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 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 Chain information for 7b5k-pdb-bundle2.pdb #53 --- Chain | Description 6 | No description available 9 | 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 x | No description available z | No description available > hide #!47 models > show #!47 models > select add #52 91305 atoms, 98560 bonds, 1 pseudobond, 7168 residues, 2 models selected > select add #53 148612 atoms, 160327 bonds, 1 pseudobond, 11690 residues, 3 models selected > ui mousemode right "translate selected models" > view matrix models > #52,1,0,0,240.48,0,1,0,-112.03,0,0,1,240.79,#53,1,0,0,240.48,0,1,0,-112.03,0,0,1,240.79 > view matrix models > #52,1,0,0,-42.627,0,1,0,-232.09,0,0,1,122.74,#53,1,0,0,-42.627,0,1,0,-232.09,0,0,1,122.74 > ui mousemode right "rotate selected models" > view matrix models > #52,0.75433,0.60612,0.25221,-144.78,-0.099152,-0.27458,0.95644,-172.8,0.64897,-0.74648,-0.14703,327.93,#53,0.75433,0.60612,0.25221,-144.78,-0.099152,-0.27458,0.95644,-172.8,0.64897,-0.74648,-0.14703,327.93 > view matrix models > #52,0.58553,0.76264,0.27483,-142.05,-0.17728,-0.21035,0.96142,-169.33,0.79103,-0.61167,0.012032,254.03,#53,0.58553,0.76264,0.27483,-142.05,-0.17728,-0.21035,0.96142,-169.33,0.79103,-0.61167,0.012032,254.03 > view matrix models > #52,0.56908,0.66591,0.4824,-161.77,-0.4301,-0.25896,0.86484,-98.677,0.70083,-0.69964,0.13904,260.96,#53,0.56908,0.66591,0.4824,-161.77,-0.4301,-0.25896,0.86484,-98.677,0.70083,-0.69964,0.13904,260.96 > view matrix models > #52,0.72575,0.65897,0.19758,-137.45,-0.31847,0.067229,0.94555,-183.39,0.6098,-0.74916,0.25865,263.32,#53,0.72575,0.65897,0.19758,-137.45,-0.31847,0.067229,0.94555,-183.39,0.6098,-0.74916,0.25865,263.32 > view matrix models > #52,-0.047118,0.96262,-0.26672,32.215,-0.66044,0.1703,0.73131,-101.82,0.74939,0.21061,0.62773,21.998,#53,-0.047118,0.96262,-0.26672,32.215,-0.66044,0.1703,0.73131,-101.82,0.74939,0.21061,0.62773,21.998 > view matrix models > #52,0.34764,0.9376,0.0070017,-80.067,-0.48952,0.17513,0.85422,-153.7,0.7997,-0.30039,0.51986,113.35,#53,0.34764,0.9376,0.0070017,-80.067,-0.48952,0.17513,0.85422,-153.7,0.7997,-0.30039,0.51986,113.35 > view matrix models > #52,0.91248,0.33236,0.23857,-125.54,-0.22854,-0.069568,0.97105,-181.94,0.33933,-0.94058,0.012477,385.04,#53,0.91248,0.33236,0.23857,-125.54,-0.22854,-0.069568,0.97105,-181.94,0.33933,-0.94058,0.012477,385.04 > view matrix models > #52,0.79824,0.56018,0.22137,-137.39,-0.28436,0.026498,0.95835,-184.6,0.53099,-0.82794,0.18045,303.13,#53,0.79824,0.56018,0.22137,-137.39,-0.28436,0.026498,0.95835,-184.6,0.53099,-0.82794,0.18045,303.13 > view matrix models > #52,-0.382,-0.49484,-0.78052,416.54,0.68811,0.41148,-0.59765,-139.25,0.61692,-0.76538,0.18332,277.46,#53,-0.382,-0.49484,-0.78052,416.54,0.68811,0.41148,-0.59765,-139.25,0.61692,-0.76538,0.18332,277.46 > view matrix models > #52,-0.40328,-0.51598,-0.75573,419.34,0.55524,0.51848,-0.65029,-123.91,0.72737,-0.68186,0.077404,263.83,#53,-0.40328,-0.51598,-0.75573,419.34,0.55524,0.51848,-0.65029,-123.91,0.72737,-0.68186,0.077404,263.83 > view matrix models > #52,0.37882,-0.89357,0.24089,169.2,0.91513,0.32286,-0.24147,-226.85,0.138,0.31191,0.94004,58.212,#53,0.37882,-0.89357,0.24089,169.2,0.91513,0.32286,-0.24147,-226.85,0.138,0.31191,0.94004,58.212 > view matrix models > #52,0.23904,-0.89157,0.38467,168.68,0.91169,0.069731,-0.40492,-156.05,0.33419,0.44749,0.8295,20.131,#53,0.23904,-0.89157,0.38467,168.68,0.91169,0.069731,-0.40492,-156.05,0.33419,0.44749,0.8295,20.131 > view matrix models > #52,0.16703,-0.074628,0.98312,-56.096,0.90276,0.41246,-0.12207,-259.6,-0.39639,0.90791,0.13626,193.27,#53,0.16703,-0.074628,0.98312,-56.096,0.90276,0.41246,-0.12207,-259.6,-0.39639,0.90791,0.13626,193.27 > view matrix models > #52,0.10696,0.041103,0.99341,-64.987,0.87864,0.46373,-0.11379,-264.64,-0.46535,0.88502,0.013484,230.72,#53,0.10696,0.041103,0.99341,-64.987,0.87864,0.46373,-0.11379,-264.64,-0.46535,0.88502,0.013484,230.72 > view matrix models > #52,0.10322,-0.08824,0.99074,-43.796,0.75489,0.65554,-0.020264,-288.17,-0.64768,0.74999,0.13428,263.73,#53,0.10322,-0.08824,0.99074,-43.796,0.75489,0.65554,-0.020264,-288.17,-0.64768,0.74999,0.13428,263.73 > ui mousemode right "translate selected models" > view matrix models > #52,0.10322,-0.08824,0.99074,171.13,0.75489,0.65554,-0.020264,-192.72,-0.64768,0.74999,0.13428,213.37,#53,0.10322,-0.08824,0.99074,171.13,0.75489,0.65554,-0.020264,-192.72,-0.64768,0.74999,0.13428,213.37 > view matrix models > #52,0.10322,-0.08824,0.99074,127.77,0.75489,0.65554,-0.020264,31.884,-0.64768,0.74999,0.13428,220.19,#53,0.10322,-0.08824,0.99074,127.77,0.75489,0.65554,-0.020264,31.884,-0.64768,0.74999,0.13428,220.19 > ui mousemode right "rotate selected models" > view matrix models > #52,0.17864,-0.009298,0.98387,103.1,0.76581,0.62914,-0.1331,53.455,-0.61776,0.77724,0.11951,213.2,#53,0.17864,-0.009298,0.98387,103.1,0.76581,0.62914,-0.1331,53.455,-0.61776,0.77724,0.11951,213.2 > undo > view matrix models > #52,0.25497,-0.30652,0.91708,147.01,0.79932,0.60052,-0.021515,32.683,-0.54413,0.73853,0.39813,158.56,#53,0.25497,-0.30652,0.91708,147.01,0.79932,0.60052,-0.021515,32.683,-0.54413,0.73853,0.39813,158.56 > ui mousemode right "move picked models" > ui mousemode right "translate selected models" > view matrix models > #52,0.25497,-0.30652,0.91708,106.7,0.79932,0.60052,-0.021515,23.276,-0.54413,0.73853,0.39813,168.11,#53,0.25497,-0.30652,0.91708,106.7,0.79932,0.60052,-0.021515,23.276,-0.54413,0.73853,0.39813,168.11 > ui mousemode right "rotate selected models" > view matrix models > #52,0.18393,-0.16763,0.96854,88.768,0.73018,0.68295,-0.02046,22.322,-0.65803,0.71097,0.24802,217.86,#53,0.18393,-0.16763,0.96854,88.768,0.73018,0.68295,-0.02046,22.322,-0.65803,0.71097,0.24802,217.86 > hide #!47 models > show #!47 models > view matrix models > #52,0.13467,-0.06139,0.98899,77.677,0.69279,0.71942,-0.049679,28.358,-0.70845,0.69185,0.13941,248.36,#53,0.13467,-0.06139,0.98899,77.677,0.69279,0.71942,-0.049679,28.358,-0.70845,0.69185,0.13941,248.36 > ui mousemode right "translate selected models" > view matrix models > #52,0.13467,-0.06139,0.98899,84.443,0.69279,0.71942,-0.049679,30.235,-0.70845,0.69185,0.13941,245.85,#53,0.13467,-0.06139,0.98899,84.443,0.69279,0.71942,-0.049679,30.235,-0.70845,0.69185,0.13941,245.85 > view matrix models > #52,0.13467,-0.06139,0.98899,83.702,0.69279,0.71942,-0.049679,30.211,-0.70845,0.69185,0.13941,238.27,#53,0.13467,-0.06139,0.98899,83.702,0.69279,0.71942,-0.049679,30.211,-0.70845,0.69185,0.13941,238.27 > select subtract #53 91305 atoms, 98560 bonds, 1 pseudobond, 7168 residues, 2 models selected > select add #53 148612 atoms, 160327 bonds, 1 pseudobond, 11690 residues, 3 models selected > select subtract #52 57307 atoms, 61767 bonds, 4522 residues, 1 model selected > select add #52 148612 atoms, 160327 bonds, 1 pseudobond, 11690 residues, 3 models selected > hide #!52 models > show #!52 models > hide #53 models > show #53 models > view matrix models > #52,0.13467,-0.06139,0.98899,80.834,0.69279,0.71942,-0.049679,34.593,-0.70845,0.69185,0.13941,244.25,#53,0.13467,-0.06139,0.98899,80.834,0.69279,0.71942,-0.049679,34.593,-0.70845,0.69185,0.13941,244.25 > ui tool show "Fit in Map" > close #1-46 > fitmap #52 inMap #47 Fit molecule 7b5k-pdb-bundle1.pdb (#52) to map cryosparc_P49_J91_006_volume_map_sharp.mrc (#47) using 91305 atoms average map value = 2.41, steps = 112 shifted from previous position = 10.2 rotated from previous position = 7.84 degrees atoms outside contour = 20130, contour level = 1 Position of 7b5k-pdb-bundle1.pdb (#52) relative to cryosparc_P49_J91_006_volume_map_sharp.mrc (#47) coordinates: Matrix rotation and translation 0.06516379 0.03028071 0.99741507 77.74188843 0.74215106 0.66669966 -0.06872716 33.75465704 -0.66705738 0.74471116 0.02097181 245.93919664 Axis 0.40986101 0.83866514 0.35868473 Axis point 132.09582672 0.00000000 106.84023825 Rotation angle (degrees) 97.09889657 Shift along axis 148.38685768 > fitmap #53 inMap #47 Fit molecule 7b5k-pdb-bundle2.pdb (#53) to map cryosparc_P49_J91_006_volume_map_sharp.mrc (#47) using 57307 atoms average map value = 1.565, steps = 108 shifted from previous position = 4.85 rotated from previous position = 7.44 degrees atoms outside contour = 19858, contour level = 1 Position of 7b5k-pdb-bundle2.pdb (#53) relative to cryosparc_P49_J91_006_volume_map_sharp.mrc (#47) coordinates: Matrix rotation and translation 0.07703747 0.03319476 0.99647549 75.17605583 0.73658953 0.67167267 -0.07932057 35.70301584 -0.67193835 0.74010405 0.02729304 247.47423149 Axis 0.41230637 0.83948863 0.35392413 Axis point 132.55303488 0.00000000 108.79904491 Rotation angle (degrees) 96.43052800 Shift along axis 148.55494477 > save "C:/Users/jlerath/Desktop/Ec24 > CryoEM/Ec24_P49_MaskMakingSessionv1_2020123.cxs" > select subtract #52 57307 atoms, 61767 bonds, 4522 residues, 1 model selected > select subtract #53 Nothing selected > ui tool show "Segment Map" > volume gaussian #47 sDev 2 Opened cryosparc_P49_J91_006_volume_map_sharp.mrc gaussian as #1, grid size 448,448,448, pixel 1.18, shown at step 1, values float32 > volume #1 level 0.09929 Segmenting cryosparc_P49_J91_006_volume_map_sharp.mrc gaussian, density threshold 0.099293 Showing 233 region surfaces 3566 watershed regions, grouped to 233 regions Showing cryosparc_P49_J91_006_volume_map_sharp gaussian.seg - 233 regions, 233 surfaces > hide #!52 models > hide #53 models > ui mousemode right select Drag select of 5264, 5311, 42941 of 45692 triangles, 5298, 5255, 5281, 769 of 37468 triangles, 5064, 27905 of 31076 triangles, 5248, 5284, 5308, 27612 of 27812 triangles, 4029, 7436 of 25388 triangles, 5279, 5246, 2560 of 28372 triangles, 5256, 5252, 23698 of 31772 triangles, 5277, 5100, 5048, 5278, 5254, 13191 of 26872 triangles, 5290, 20732 of 27164 triangles, 5305, 5269, 5263, 11035 of 22624 triangles, 5313, 5226, 5328, 271 of 22148 triangles, 5027, 5046, 5282, 5324, 5325, 19891 of 24132 triangles, 5050, 5285, 5266, 4229 of 21992 triangles, 5005, 5327, 5346, 5076, 19483 of 21880 triangles, 5261, 5141, 5306, 18264 of 22580 triangles, 5343, 5348, 5022, 5258, 5344, 16313 of 19248 triangles, 5330, 7160 of 18940 triangles, 5140, 1087 of 22784 triangles, 5194, 11334 of 18612 triangles, 5013, 5283, 11929 of 17332 triangles, 5265, 5289, 5334, 9410 of 18772 triangles, 4629, 1061 of 13748 triangles, 4849, 1245 of 14028 triangles, 5349, 3974, 5340, 5052, 5262, 5049, 5116, 5109, 2387 of 13220 triangles, 5034, 5268, 5179, 1120 of 14844 triangles, 5089, 6304 of 13136 triangles, 5079, 5342, 8333 of 13464 triangles, 5331, 32 of 13008 triangles, 4498, 5122, 5146, 5210, 4986, 4614, 269 of 11364 triangles, 5323, 5186, 10848 of 11264 triangles, 4134, 10511 of 11104 triangles, 3624, 5187, 8905 of 10392 triangles, 5075, 4162, 4751, 6698 of 9044 triangles, 5015, 4998, 338, 5223, 5214, 5136, 5188, 7929 of 9104 triangles, 4989, 4694, 42 of 8988 triangles, 4869, 4961, 6276 of 7884 triangles, 5007, 4910, 4480, 5225, 1 cryosparc_P49_J91_006_volume_map_sharp.mrc gaussian > select clear Drag select of 5264, 39151 of 45140 triangles, 5311, 16779 of 45692 triangles, 5298, 5255, 39096 of 39100 triangles, 5064, 24739 of 31076 triangles, 5248, 5284, 18237 of 30028 triangles, 5308, 19507 of 27812 triangles, 4029, 7176 of 25388 triangles, 5279, 5256, 21592 of 27668 triangles, 5277, 5100, 26863 of 27108 triangles, 5048, 5278, 21388 of 28712 triangles, 5290, 275 of 27164 triangles, 5305, 5269, 6159 of 26028 triangles, 5263, 159 of 22624 triangles, 5313, 20311 of 23028 triangles, 5226, 5027, 16631 of 23316 triangles, 5046, 19519 of 19708 triangles, 5282, 5324, 5325, 4836 of 24132 triangles, 5050, 5285, 5005, 23475 of 23556 triangles, 5327, 14960 of 21348 triangles, 5346, 25432 of 29400 triangles, 5076, 5901 of 21880 triangles, 5261, 5141, 15928 of 22324 triangles, 5306, 5286 of 22580 triangles, 5343, 5348, 13054 of 20716 triangles, 5022, 5258, 5344, 913 of 19248 triangles, 5330, 1989 of 18940 triangles, 5194, 3287 of 18612 triangles, 5013, 5283, 1481 of 17332 triangles, 5265, 5289, 5349, 10789 of 15180 triangles, 3974, 5340, 5052, 5262, 5049, 5116, 5034, 6144 of 13640 triangles, 5268, 5089, 884 of 13136 triangles, 5079, 10460 of 15140 triangles, 4498, 5122, 5146, 12058 of 13704 triangles, 5210, 10125 of 13964 triangles, 4986, 10502 of 11420 triangles, 5323, 12958 of 14240 triangles, 4134, 5814 of 11104 triangles, 3624, 5187, 1201 of 10392 triangles, 5075, 4162, 5355 of 11024 triangles, 5015, 4998, 9156 of 9952 triangles, 338, 5223, 4223 of 9640 triangles, 5214, 1367 of 9020 triangles, 5136, 1854 of 9632 triangles, 5188, 2341 of 9104 triangles, 4989, 4869, 8312 of 8332 triangles, 5007, 4910, 4480, 5225, 1 cryosparc_P49_J91_006_volume_map_sharp.mrc gaussian > select clear Drag select of 5264, 15208 of 45140 triangles, 5311, 2183 of 45692 triangles, 5298, 34240 of 36192 triangles, 5255, 5064, 24569 of 31076 triangles, 5248, 5284, 26557 of 30028 triangles, 5308, 26000 of 27812 triangles, 5279, 5256, 11159 of 27668 triangles, 5252, 3757 of 31772 triangles, 5277, 5100, 5048, 5278, 28655 of 28712 triangles, 5254, 379 of 26872 triangles, 5305, 5269, 13523 of 26028 triangles, 5263, 5383 of 22624 triangles, 5313, 20791 of 23028 triangles, 5226, 5027, 20827 of 23316 triangles, 5046, 19574 of 19708 triangles, 5282, 5324, 5325, 6361 of 24132 triangles, 5050, 13405 of 20640 triangles, 5285, 20125 of 22456 triangles, 5005, 5327, 12719 of 21348 triangles, 5346, 16360 of 29400 triangles, 5076, 13530 of 21880 triangles, 5261, 16084 of 20052 triangles, 5141, 22233 of 22324 triangles, 5306, 2692 of 22580 triangles, 5343, 5348, 15677 of 20716 triangles, 5022, 19765 of 21692 triangles, 5258, 5330, 134 of 18940 triangles, 5194, 3529 of 18612 triangles, 5013, 14662 of 16160 triangles, 5265, 5289, 5349, 3824 of 15180 triangles, 3974, 5340, 5052, 3770 of 15720 triangles, 5262, 5049, 12279 of 15968 triangles, 5116, 5034, 8063 of 13640 triangles, 5268, 5079, 11692 of 15140 triangles, 4498, 5122, 5146, 8140 of 13704 triangles, 5210, 605 of 13964 triangles, 4986, 8239 of 11420 triangles, 5323, 9341 of 14240 triangles, 5186, 2958 of 11264 triangles, 4134, 8250 of 11104 triangles, 3624, 5075, 625 of 10484 triangles, 4751, 1349 of 9044 triangles, 5015, 4998, 7873 of 9952 triangles, 338, 5223, 705 of 9640 triangles, 5214, 3946 of 9020 triangles, 4989, 4869, 5007, 5623 of 8696 triangles, 4910, 4480, 7323 of 7648 triangles, 5225, 1 cryosparc_P49_J91_006_volume_map_sharp.mrc gaussian > select #2.162 1 model selected > undo > select add #2.162 79 models selected > select subtract #1 77 models selected > hide #!1 models > show #!52 models > hide #!52 models > show #53 models > select subtract #2.135 76 models selected > hide #53 models > select add #2.220 77 models selected > show #53 models > hide #53 models > show #53 models > select add #2.126 78 models selected Grouped 78 regions > hide #2.3 models > select #2.214 1 model selected > select #2.102 1 model selected > show #2.3 models > select #2.3 1 model selected > select #2.3 1 model selected Ungrouped to 78 regions > hide #53 models > show #!52 models > select subtract #2.80 77 models selected > show #53 models > hide #!52 models > select add #2.209 78 models selected > select add #2.97 79 models selected > select add #2.47 80 models selected > hide #53 models > show #!52 models > show #53 models > hide #53 models > hide #!52 models > show #53 models > select add #2.74 81 models selected > hide #53 models > show #!52 models > hide #!52 models > show #53 models > select add #2.108 82 models selected > hide #53 models > show #!52 models > undo [Repeated 7 time(s)] > hide #53 models > show #!52 models > select add #52/A:1915@O4 1 atom, 1 residue, 82 models selected > select subtract #52/A:1915@O4 81 models selected > show #2.108 models > select subtract #2.101 80 models selected > select add #2.101 81 models selected > select subtract #2.101 80 models selected Grouped 80 regions > select #2.101 1 model selected Ungrouped to 3 regions > select #2.4 1 model selected > select #2.9 1 model selected > select #2.4 1 model selected > select #2.3 1 model selected Ungrouped to 80 regions > select add #2.4 81 models selected > hide #!52 models > show #53 models > select add #2.108 82 models selected > hide #53 models > show #!52 models > select subtract #2.108 81 models selected > select add #2.108 82 models selected > select subtract #2.108 81 models selected > show #53 models > hide #!52 models Grouped 81 regions > select #2.108 1 model selected > hide #53 models > show #!52 models > show #53 models > hide #!52 models Ungrouped to 3 regions > select #2.4 1 model selected Ungrouped to 2 regions > select #2.23 1 model selected > select #2.3 1 model selected Ungrouped to 81 regions > select add #2.23 82 models selected Grouped 82 regions > select subtract #2.199 155 models selected > select subtract #2.211 154 models selected > hide #53 models > show #!52 models > hide #!52 models > show #53 models > select #2.199 1 model selected > select #2.211 1 model selected Ungrouped to 2 regions > select #2.4 1 model selected > select add #2.199 2 models selected > select #2.3 1 model selected Ungrouped to 82 regions > select add #2.199 83 models selected > select add #2.4 84 models selected Grouped 84 regions > select #2.23 1 model selected > hide #53 models > show #!52 models > select #2.23 1 model selected > select add #2.3 2 models selected > hide #!52 models > show #53 models > select #2.112 1 model selected > select add #2.226 2 models selected > select add #2.69 3 models selected > select subtract #2.226 2 models selected > select subtract #2.69 1 model selected > select #2.187 1 model selected > select #2.39 1 model selected > select add #2.99 2 models selected > select #2.39 1 model selected > select #2.99 1 model selected Ungrouped to 3 regions > select #2.29 1 model selected > select #2.31 1 model selected > select #2.39 1 model selected > select #2.29 1 model selected > select #2.187 1 model selected > undo [Repeated 1 time(s)] > select #53/g:52@CD 1 atom, 1 residue, 1 model selected > select #2.3 1 model selected > select #2.25 1 model selected > select #2.30 1 model selected > select #2.151 1 model selected > select #2.123 1 model selected > select #2.132 1 model selected > select #2.217 1 model selected > select #2.134 1 model selected > select #2.3 1 model selected Ungrouped to 84 regions > select subtract #2.225 83 models selected Grouped 83 regions > select #2.225 1 model selected Ungrouped to 2 regions > select #2.32 1 model selected Ungrouped to 2 regions > select #2.35 1 model selected > select #2.36 1 model selected > select #2.3 1 model selected > select #53/i:36@CD 1 atom, 1 residue, 1 model selected Ungrouped to 179 regions > select #2.3 1 model selected > select add #2.36 2 models selected > select add #2.34 3 models selected Grouped 3 regions > select #2.80 1 model selected Ungrouped to 5 regions > select #2.6 1 model selected > select #2.7 1 model selected > select #2.10 1 model selected > select #2.7 1 model selected Ungrouped to 0 regions > select #2.10 1 model selected Ungrouped to 0 regions > select #2.6 1 model selected > select add #2.1 2 models selected Grouped 2 regions > select add #2 273 models selected > select subtract #2 Nothing selected > select #2.1 1 model selected > select clear > select #2.1 1 model selected > show #!52 models > hide #53 models > select subtract #2.14 270 models selected > hide #!52 models > show #53 models > select #2.14 1 model selected > select #2.1 1 model selected Grouped 1 regions > select #2.14 1 model selected > select #2.1 1 model selected > select #2.14 1 model selected > select add #2.1 2 models selected Grouped 2 regions > select #2.23 1 model selected Ungrouped to 0 regions > select #2.23 1 model selected > hide #53 models > show #!52 models > hide #2.1 models > hide #!52 models > show #53 models > select #2.194 1 model selected > select add #2.35 2 models selected > select add #2.134 3 models selected > select add #2.112 4 models selected > select add #2.187 5 models selected > select add #53/x:21@C5 1 atom, 1 residue, 6 models selected > select subtract #53/x:21@C5 5 models selected > select add #2.151 6 models selected > select add #2.172 7 models selected > select add #2.225 8 models selected > select add #2.230 9 models selected > select add #2.155 10 models selected > select add #2.245 11 models selected Grouped 11 regions > select #2.102 1 model selected > select #2.223 1 model selected > show #2.102 models > select #2.102 1 model selected > select #2.102 1 model selected Ungrouped to 5 regions > select #2.6 1 model selected > select #2.15 1 model selected Ungrouped to 7 regions > select #2.6 1 model selected > select #2.30 1 model selected Ungrouped to 2 regions > select #2.15 1 model selected Ungrouped to 0 regions > select #53/z:44@C1' 1 atom, 1 residue, 1 model selected > select #2.6 1 model selected > select #2.29 1 model selected > select #2.31 1 model selected Ungrouped to 3 regions > select #2.35 1 model selected > select #2.34 1 model selected Ungrouped to 4 regions > select #2.38 1 model selected > select #2.37 1 model selected > select #2.31 1 model selected Ungrouped to 0 regions > show #2.29 models > hide #2.29 models > show #2.37 models > select #2.37 1 model selected Ungrouped to 0 regions > select #2.37 1 model selected > select #2.6 1 model selected > select #2.217 1 model selected > select #2.86 1 model selected > select #2.132 1 model selected > select #53/x:17@O4 1 atom, 1 residue, 1 model selected > select #2.217 1 model selected > select #2.6 1 model selected Grouped 1 regions > select #2.217 1 model selected > select #2.6 1 model selected > select #2.217 1 model selected > select add #2.6 2 models selected Grouped 2 regions > select #2.331 1 model selected > select #2.333 1 model selected > select #2.148 1 model selected > select #2.68 1 model selected > undo [Repeated 2 time(s)] > show #2.148 models > select #2.148 1 model selected Ungrouped to 4 regions > select #2.41 1 model selected > select #2.34 1 model selected > select #2.68 1 model selected > select #2.34 1 model selected > select #2.334 1 model selected Ungrouped to 2 regions > select #2.44 1 model selected Ungrouped to 4 regions > select #2.48 1 model selected Ungrouped to 0 regions > select #2.6 1 model selected > select clear > select #2.6 1 model selected > select #2.39 1 model selected Ungrouped to 2 regions > select #2.52 1 model selected > select #2.44 1 model selected Ungrouped to 2 regions > select #2.53 1 model selected > select #2.63 1 model selected > select #2.132 1 model selected Ungrouped to 6 regions > select #2.62 1 model selected Ungrouped to 0 regions Drag select of 5151, 6 of 13276 triangles, 5218, 17 of 13032 triangles, 4665, 6 of 10212 triangles, 5107, 15 of 32808 triangles, 5176, 21 of 21772 triangles, 5119, 12 of 13596 triangles, 5044, 12 of 10544 triangles, 4944, 8 of 4912 triangles, 1825, 5 of 6552 triangles, 4873, 6 of 5760 triangles > select #2.65 1 model selected > select #2.15 1 model selected Ungrouped to 0 regions > select #2.35 1 model selected > select #2.38 1 model selected > select #2.259 1 model selected > select #53/9:74@O3' 1 atom, 1 residue, 1 model selected > select #2.37 1 model selected Ungrouped to 0 regions > select #2.37 1 model selected > select #53/9:75@OP1 1 atom, 1 residue, 1 model selected > select #2.31 1 model selected > select #2.36 1 model selected > select #2.6 1 model selected > select #2.252 1 model selected > select #2.335 1 model selected > select #2.46 1 model selected > select #2.43 1 model selected > select #2.48 1 model selected > select #2.49 1 model selected > select #2.50 1 model selected > select #2.48 1 model selected > select #2.41 1 model selected > select #2.171 1 model selected > select add #2.6 2 models selected Grouped 2 regions > select #53/z:74@P 1 atom, 1 residue, 1 model selected > select #53/z:74@OP2 1 atom, 1 residue, 1 model selected > select #2.62 1 model selected > select #2.53 1 model selected > select #2.52 1 model selected > select #2.62 1 model selected Ungrouped to 0 regions > select #2.62 1 model selected > select #2.23 1 model selected Ungrouped to 0 regions > select #2.1 1 model selected > select add #2.6 2 models selected Grouped 287 regions > select #2.2 1 model selected > select #2.1 1 model selected > select #2.6 1 model selected > hide #53 models > show #!52 models > select #2.1 1 model selected > select add #2.6 2 models selected > select #2.2 1 model selected Ungrouped to 287 regions > select subtract #2.166 286 models selected Grouped 286 regions > select #2.1 1 model selected Ungrouped to 2 regions > hide #!52 models > select #2.3 1 model selected Ungrouped to 1 regions > select #2.1 1 model selected Ungrouped to 2 regions > select #2.3 1 model selected Ungrouped to 3 regions > select #2.8 1 model selected Ungrouped to 83 regions > select #2.62 1 model selected > undo > show #53 models > hide #53 models > show #!52 models > show #2.2 models > hide #2.2 models > hide #!52 models > show #53 models > select add #2.5 84 models selected > select add #2.166 85 models selected > select add #2.4 86 models selected > select add #2.1 87 models selected > select add #2.7 88 models selected > select subtract #2.52 87 models selected > hide #53 models > show #!52 models Grouped 87 regions > hide #!52 models > show #53 models > select #2.52 1 model selected Ungrouped to 2 regions > select #2.4 1 model selected > select #2.3 1 model selected > select add #2.1 2 models selected Grouped 2 regions > select add #2.6 2 models selected Grouped 2 regions > hide #2.2 models > show #2.2 models > hide #53 models > show #!52 models > hide #2.6 models > show #2.6 models > hide #2.6 models > select subtract #2.2 Nothing selected > hide #2.2 models > show #2.2 models > hide #2.1 models > show #2.1 models > show #2.6 models > save "C:/Users/jlerath/Desktop/Ec24 > CryoEM/Ec24_P49_MaskMakingSessionv2_2020123.cxs" > hide #!52 models > select #2.2 1 model selected Saving 1 regions to mrc file... Opened cryosparc_P49_J91_50SMask_20250123.mrc as #3, grid size 202,193,156, pixel 1.18, shown at step 1, values float32 Wrote cryosparc_P49_J91_50SMask_20250123.mrc > select #2.1 1 model selected Saving 1 regions to mrc file... Opened cryosparc_P49_J91_30SMask_20250123.mrc as #4, grid size 162,203,117, pixel 1.18, shown at step 1, values float32 Wrote cryosparc_P49_J91_30SMask_20250123.mrc > select #2.6 1 model selected Saving 1 regions to mrc file... Opened cryosparc_P49_J91_APEMask_20250123.mrc as #5, grid size 97,78,96, pixel 1.18, shown at step 1, values float32 Wrote cryosparc_P49_J91_APEMask_20250123.mrc > hide #!2 models > volume #3 level 0.1107 > volume #4 level 0.1064 > volume #4 level 0.1 > volume #4 level 0.11 > volume #4 level 0.105 > volume #3 level 0.105 > volume #5 level 0.105 > volume onesmask #3 onGrid #47 fullMap true valueType float32 Opened cryosparc_P49_J91_006_volume_map_sharp.mrc masked as #6, grid size 448,448,448, pixel 1.18, shown at step 1, values float32 > hide #!3 models > volume #6 level 0.3841 > volume #6 level 0.5 > save "C:/Users/jlerath/Desktop/Ec24 > CryoEM/Ec24_P49_MaskMakingSessionv2_2020123.cxs" No map chosen to save > save "C:/Users/jlerath/Desktop/Ec24 > CryoEM/Masks/J91/cryosparc_P49_J91_50SMasked_20250123.mrc" models #6 > volume onesmask #4 onGrid #47 fullMap true valueType float32 Opened cryosparc_P49_J91_006_volume_map_sharp.mrc masked as #7, grid size 448,448,448, pixel 1.18, shown at step 1, values float32 > hide #!4 models > select add #2 4 models selected > select subtract #2 Nothing selected > volume onesmask #5 onGrid #47 fullMap true valueType float32 Opened cryosparc_P49_J91_006_volume_map_sharp.mrc masked as #8, grid size 448,448,448, pixel 1.18, shown at step 1, values float32 > hide #!5 models > save "C:/Users/jlerath/Desktop/Ec24 > CryoEM/Masks/J91/cryosparc_P49_J91_30SMasked_20250123.mrc" models #7 > save "C:/Users/jlerath/Desktop/Ec24 > CryoEM/Masks/J91/cryosparc_P49_J91_APEMasked_20250123.mrc" models #8 > volume resample #3 onGrid #47 Opened cryosparc_P49_J91_50SMask_20250123.mrc resampled as #9, grid size 448,448,448, pixel 1.18, shown at step 1, values float32 > save "C:/Users/jlerath/Desktop/Ec24 > CryoEM/Masks/J91/cryosparc_P49_J91_50SMask_20250123.mrc" models #9 > close #3 > volume resample #4 onGrid #47 Opened cryosparc_P49_J91_30SMask_20250123.mrc resampled as #3, grid size 448,448,448, pixel 1.18, shown at step 1, values float32 > volume resample #5 onGrid #47 Opened cryosparc_P49_J91_APEMask_20250123.mrc resampled as #10, grid size 448,448,448, pixel 1.18, shown at step 1, values float32 > close #4-5 > save "C:/Users/jlerath/Desktop/Ec24 > CryoEM/Masks/J91/cryosparc_P49_J91_30SMask_20250123.mrc" models #3 > save "C:/Users/jlerath/Desktop/Ec24 > CryoEM/Masks/J91/cryosparc_P49_J91_APEMask_20250123.mrc" models #10 > save "C:/Users/jlerath/Desktop/Ec24 > CryoEM/Ec24_P49_MaskMakingSessionv2_2020123.cxs" > volume resample #3,10 volume resample must specify onGrid option or spacing option > vop maximum #3,10 Opened volume maximum as #4, grid size 448,448,448, pixel 1.18, shown at step 1, values float32 > save "C:/Users/jlerath/Desktop/Ec24 > CryoEM/Masks/J91/cryosparc_P49_J91_30SAPEMask_20250123.mrc" models #4 > save "C:/Users/jlerath/Desktop/Ec24 > CryoEM/Ec24_P49_MaskMakingSessionv2_2020123.cxs" > hide #!9 models > show #!9 models > vop maximum #9,10 Opened volume maximum as #5, grid size 448,448,448, pixel 1.18, shown at step 1, values float32 > save "C:/Users/jlerath/Desktop/Ec24 > CryoEM/Ec24_P49_MaskMakingSessionv2_2020123.cxs" ——— End of log from Thu Jan 23 17:30:05 2025 ——— opened ChimeraX session Showing cryosparc_P49_J91_006_volume_map_sharp gaussian.seg - 3 regions, 3 surfaces > close #1-10,47-51 > open "C:/Users/jlerath/Desktop/Ec24 > CryoEM/cryosparc_P49_J120_004_volume_map_sharp.mrc" > "C:/Users/jlerath/Desktop/Ec24 > CryoEM/cryosparc_P49_J119_004_volume_map_sharp.mrc" > "C:/Users/jlerath/Desktop/Ec24 > CryoEM/cryosparc_P49_J118_003_volume_map_sharp.mrc" > "C:/Users/jlerath/Desktop/Ec24 > CryoEM/cryosparc_P49_J117_004_volume_map_sharp.mrc" Opened cryosparc_P49_J120_004_volume_map_sharp.mrc as #1.1, grid size 448,448,448, pixel 1.18, shown at level 0.66, step 2, values float32 Opened cryosparc_P49_J119_004_volume_map_sharp.mrc as #1.2, grid size 448,448,448, pixel 1.18, shown at level 0.875, step 2, values float32 Opened cryosparc_P49_J118_003_volume_map_sharp.mrc as #1.3, grid size 448,448,448, pixel 1.18, shown at level 0.849, step 2, values float32 Opened cryosparc_P49_J117_004_volume_map_sharp.mrc as #1.4, grid size 448,448,448, pixel 1.18, shown at level 0.628, step 2, values float32 > volume #1 step 1 > surface dust #1 size 10 > save "C:/Users/jlerath/Desktop/Ec24 > CryoEM/P49_Ec24_7b5k_fitting_20250127.cxs" > hide #!1.4 models > hide #!1.3 models > show #!1.3 models > hide #!1.1 models > show #!52 models > select add #52 91305 atoms, 98560 bonds, 1 pseudobond, 7168 residues, 2 models selected > hide #!1.3 models > hide #!1.2 models > show #!1.2 models > show #!1.3 models > hide #!1 models > nucleotides (#!52 & sel) slab > hide (#!52 & sel) target a > cartoon (#!52 & sel) > nucleotides (#!52 & sel) slab > style (#!52 & sel) ball Changed 91305 atom styles > nucleotides (#!52 & sel) ladder > select #52 91305 atoms, 98560 bonds, 1 pseudobond, 7168 residues, 2 models selected > select subtract #52 Nothing selected > select #52 91305 atoms, 98560 bonds, 1 pseudobond, 7168 residues, 2 models selected > style (#!52 & sel) ball Changed 91305 atom styles > cartoon hide (#!52 & sel) > show (#!52 & sel) target ab > select subtract #52 Nothing selected > select add #52 91305 atoms, 98560 bonds, 1 pseudobond, 7168 residues, 2 models selected > style (#!52 & sel) sphere Changed 91305 atom styles > style (#!52 & sel) stick Changed 91305 atom styles > style sel sphere Changed 91305 atom styles > style (#!52 & sel) stick Changed 91305 atom styles > cartoon style (#!52 & sel) modeHelix tube sides 20 > style (#!52 & sel) ringFill thin Changed 7168 residue ring styles > select subtract #52 Nothing selected > select #52/A 63107 atoms, 69726 bonds, 1 pseudobond, 3745 residues, 2 models selected > hide #!52 models > show #52/A > show #!52/A > show #!52 models > hide #!52 models > show #!52 models > show #52 > hide #52 > show #52 /A > select add #52 91305 atoms, 98560 bonds, 1 pseudobond, 7168 residues, 2 models selected > select subtract #52 Nothing selected > select #52 /A 63107 atoms, 69726 bonds, 1 pseudobond, 3745 residues, 2 models selected > show (#!52 & sel-residues & sidechain) target ab > hide (#!52 & sel) target a > show (#!52 & sel-residues & sidechain) target ab > nucleotides (#!52 & sel) atoms > show (#!52 & sel) target ab > hide (#!52 & sel) target a > hide (#!52 & sel-residues & (protein|nucleic)) target a > cartoon hide (#!52 & sel-residues) > show (#!52 & sel-residues & backbone) target ab > show (#!52 & sel-residues & sidechain) target ab > nucleotides (#!52 & sel) slab > cartoon style (#!52 & sel) xsection oval modeHelix default > nucleotides (#!52 & sel) atoms [Repeated 1 time(s)] > nucleotides (#!52 & sel) fill > nucleotides (#!52 & sel) atoms > select add #52 91305 atoms, 98560 bonds, 1 pseudobond, 7168 residues, 2 models selected > select subtract #52 Nothing selected > show #!1 models > ui tool show "Fit in Map" > fitmap #52 inMap #1.1 Fit molecule 7b5k-pdb-bundle1.pdb (#52) to map cryosparc_P49_J120_004_volume_map_sharp.mrc (#1.1) using 91305 atoms average map value = 0.05267, steps = 120 shifted from previous position = 0.713 rotated from previous position = 0.771 degrees atoms outside contour = 89857, contour level = 0.6597 Position of 7b5k-pdb-bundle1.pdb (#52) relative to cryosparc_P49_J120_004_volume_map_sharp.mrc (#1.1) coordinates: Matrix rotation and translation 0.07819699 0.02858518 0.99652806 75.58436069 0.73970593 0.66848510 -0.07721964 35.26127183 -0.66837148 0.74317604 0.03112889 244.65588013 Axis 0.41275283 0.83763483 0.35777504 Axis point 131.40698979 0.00000000 107.11590407 Rotation angle (degrees) 96.37841305 Shift along axis 148.26549702 > fitmap #52 inMap #1.3 Fit molecule 7b5k-pdb-bundle1.pdb (#52) to map cryosparc_P49_J118_003_volume_map_sharp.mrc (#1.3) using 91305 atoms average map value = 2.342, steps = 52 shifted from previous position = 0.774 rotated from previous position = 0.729 degrees atoms outside contour = 17440, contour level = 0.84917 Position of 7b5k-pdb-bundle1.pdb (#52) relative to cryosparc_P49_J118_003_volume_map_sharp.mrc (#1.3) coordinates: Matrix rotation and translation 0.06589855 0.03024096 0.99736800 77.70893652 0.74208771 0.66671640 -0.06924690 33.85592583 -0.66705567 0.74469779 0.02149420 245.88277579 Axis 0.41008346 0.83857371 0.35864425 Axis point 132.08889584 0.00000000 106.83039621 Rotation angle (degrees) 97.06212189 Shift along axis 148.44228139 > volume #1.2 style mesh > volume #1.3 style mesh > volume #1.2 color #00aaff > volume #1.3 color #55aaff > transparency #1.1,1.3 50 > transparency #1.1 50 > transparency #1.2 50 > show #!1.1 models > hide #!1.1 models > show #!1.1 models > hide #!1.1 models > hide #!1.3 models > volume #1.2 style surface > save "C:/Users/jlerath/Desktop/Ec24 > CryoEM/P49_Ec24_7b5k_fitting_20250127.cxs" > hide #!1.2 models > hide #!52 models > show #53 models > show #!1.4 models > show #!1.3 models > hide #!1.3 models > show #!1.1 models > fitmap #53 inMap #1.1 Fit molecule 7b5k-pdb-bundle2.pdb (#53) to map cryosparc_P49_J120_004_volume_map_sharp.mrc (#1.1) using 57307 atoms average map value = 1.794, steps = 48 shifted from previous position = 0.189 rotated from previous position = 0.267 degrees atoms outside contour = 13150, contour level = 0.6597 Position of 7b5k-pdb-bundle2.pdb (#53) relative to cryosparc_P49_J120_004_volume_map_sharp.mrc (#1.1) coordinates: Matrix rotation and translation 0.08065648 0.03062497 0.99627140 74.67240789 0.73555791 0.67269467 -0.08022790 36.08441918 -0.67264341 0.73928619 0.03173074 246.93484187 Axis 0.41214354 0.83931744 0.35451930 Axis point 132.36293280 0.00000000 108.66644642 Rotation angle (degrees) 96.16886189 Shift along axis 148.60520000 > fitmap #53 inMap #1.4 Fit molecule 7b5k-pdb-bundle2.pdb (#53) to map cryosparc_P49_J117_004_volume_map_sharp.mrc (#1.4) using 57307 atoms average map value = 1.834, steps = 28 shifted from previous position = 0.0544 rotated from previous position = 0.0554 degrees atoms outside contour = 10945, contour level = 0.6279 Position of 7b5k-pdb-bundle2.pdb (#53) relative to cryosparc_P49_J117_004_volume_map_sharp.mrc (#1.4) coordinates: Matrix rotation and translation 0.07997953 0.03100243 0.99631430 74.79269903 0.73596465 0.67227689 -0.07999918 35.98189076 -0.67227923 0.73965039 0.03095170 246.91111601 Axis 0.41225385 0.83924172 0.35457030 Axis point 132.34436872 0.00000000 108.61919910 Rotation angle (degrees) 96.22285650 Shift along axis 148.57843096 > hide #!1.1 models > hide #!1.4 models > show #!1.4 models > show #!1.1 models > hide #!1.1 models > color #1.4 yellow models > color #1.1 #ffff7f80 models > hide #!1.4 models > show #!1.1 models > hide #!1.1 models > open "C:/Users/jlerath/Desktop/Ec24 > CryoEM/J117_004_volume_map_deepEMhancer.mrc" Opened J117_004_volume_map_deepEMhancer.mrc as #2, grid size 448,448,448, pixel 1.18, shown at level 0.000847, step 2, values float32 > volume #2 step 1 > volume #2 level 0.1 > volume #2 level 0.01 > hide #53 models > volume #2 level 0.1 > show #53 models > fitmap #53 inMap #2 Fit molecule 7b5k-pdb-bundle2.pdb (#53) to map J117_004_volume_map_deepEMhancer.mrc (#2) using 57307 atoms average map value = 0.3279, steps = 44 shifted from previous position = 0.0166 rotated from previous position = 0.0235 degrees atoms outside contour = 15687, contour level = 0.1 Position of 7b5k-pdb-bundle2.pdb (#53) relative to J117_004_volume_map_deepEMhancer.mrc (#2) coordinates: Matrix rotation and translation 0.07998938 0.03097653 0.99631431 74.77773471 0.73624109 0.67197384 -0.08000174 35.95882931 -0.67197531 0.73992681 0.03094457 246.81483673 Axis 0.41240097 0.83910270 0.35472821 Axis point 132.27815784 0.00000000 108.58763036 Rotation angle (degrees) 96.23151134 Shift along axis 148.56374687 > fitmap #53 inMap #2 Fit molecule 7b5k-pdb-bundle2.pdb (#53) to map J117_004_volume_map_deepEMhancer.mrc (#2) using 57307 atoms average map value = 0.3279, steps = 40 shifted from previous position = 0.0045 rotated from previous position = 0.00287 degrees atoms outside contour = 15675, contour level = 0.1 Position of 7b5k-pdb-bundle2.pdb (#53) relative to J117_004_volume_map_deepEMhancer.mrc (#2) coordinates: Matrix rotation and translation 0.08003576 0.03096208 0.99631104 74.76783588 0.73624689 0.67196451 -0.08002671 35.96165032 -0.67196343 0.73993588 0.03098545 246.80805264 Axis 0.41241633 0.83909149 0.35473688 Axis point 132.27346497 0.00000000 108.58920973 Rotation angle (degrees) 96.22926572 Shift along axis 148.56250897 > fitmap #53 inMap #2 Fit molecule 7b5k-pdb-bundle2.pdb (#53) to map J117_004_volume_map_deepEMhancer.mrc (#2) using 57307 atoms average map value = 0.3279, steps = 40 shifted from previous position = 0.00203 rotated from previous position = 0.00103 degrees atoms outside contour = 15677, contour level = 0.1 Position of 7b5k-pdb-bundle2.pdb (#53) relative to J117_004_volume_map_deepEMhancer.mrc (#2) coordinates: Matrix rotation and translation 0.08003506 0.03097556 0.99631068 74.76752829 0.73623825 0.67197301 -0.08003489 35.96483317 -0.67197299 0.73992760 0.03097600 246.81141071 Axis 0.41241631 0.83909618 0.35472578 Axis point 132.27436638 0.00000000 108.59096248 Rotation angle (degrees) 96.22931314 Shift along axis 148.56367309 > fitmap #53 inMap #2 Fit molecule 7b5k-pdb-bundle2.pdb (#53) to map J117_004_volume_map_deepEMhancer.mrc (#2) using 57307 atoms average map value = 0.3279, steps = 40 shifted from previous position = 0.00321 rotated from previous position = 0.00275 degrees atoms outside contour = 15674, contour level = 0.1 Position of 7b5k-pdb-bundle2.pdb (#53) relative to J117_004_volume_map_deepEMhancer.mrc (#2) coordinates: Matrix rotation and translation 0.08000372 0.03099797 0.99631250 74.76985197 0.73625808 0.67195214 -0.08002763 35.96488568 -0.67195499 0.73994561 0.03093616 246.81304322 Axis 0.41242381 0.83909229 0.35472628 Axis point 132.27139427 0.00000000 108.59184575 Rotation angle (degrees) 96.23196578 Shift along axis 148.56579808 Average map value = 0.3279 for 57307 atoms, 15674 outside contour > fitmap #53 inMap #2 Fit molecule 7b5k-pdb-bundle2.pdb (#53) to map J117_004_volume_map_deepEMhancer.mrc (#2) using 57307 atoms average map value = 0.3279, steps = 44 shifted from previous position = 0.0108 rotated from previous position = 0.00674 degrees atoms outside contour = 15664, contour level = 0.1 Position of 7b5k-pdb-bundle2.pdb (#53) relative to J117_004_volume_map_deepEMhancer.mrc (#2) coordinates: Matrix rotation and translation 0.08004318 0.03101902 0.99630867 74.74917467 0.73618156 0.67203122 -0.08006762 35.97720625 -0.67203412 0.73987292 0.03095588 246.83246729 Axis 0.41240423 0.83912380 0.35467451 Axis point 132.27746568 0.00000000 108.60863843 Rotation angle (degrees) 96.22798152 Shift along axis 148.56138974 > hide #53 models > hide #!2 models > show #!1.1 models > hide #!1.1 models > show #!1.2 models > show #!52 models > ui tool show "Show Sequence Viewer" > sequence chain #52/A Alignment identifier is 52/A > select #52/A:2563 20 atoms, 21 bonds, 1 residue, 1 model selected > select #52/A:2563 20 atoms, 21 bonds, 1 residue, 1 model selected > select #52/A:2063 20 atoms, 21 bonds, 1 residue, 1 model selected > select #52/A:2063 20 atoms, 21 bonds, 1 residue, 1 model selected > select #52/A:2057 23 atoms, 25 bonds, 1 residue, 1 model selected > select #52/A:2057 23 atoms, 25 bonds, 1 residue, 1 model selected > volume #1.3 style surface > save "C:/Users/jlerath/Desktop/Ec24 > CryoEM/P49_Ec24_7b5k_fitting_20250127.cxs" ——— End of log from Mon Jan 27 14:19:42 2025 ——— opened ChimeraX session > close #1-2#1.1-4 > open "C:/Users/jlerath/Desktop/Ec24 > CryoEM/cryosparc_P49_J119_004_volume_map.mrc" Opened cryosparc_P49_J119_004_volume_map.mrc as #1, grid size 448,448,448, pixel 1.18, shown at level 0.217, step 2, values float32 > volume #1 step 1 > close #1 > open "C:/Users/jlerath/Desktop/Ec24 > CryoEM/cryosparc_P49_J119_004_volume_map_sharp.mrc" Opened cryosparc_P49_J119_004_volume_map_sharp.mrc as #1, grid size 448,448,448, pixel 1.18, shown at level 0.875, step 2, values float32 > volume #1 step 1 > surface dust #1 size 10 > isolde start > set selectionWidth 4 Done loading forcefield > isolde set simFidelityMode Medium/Medium ISOLDE: setting sim fidelity mode to Medium/Medium nonbonded_cutoff_distance = 0.900000 use_gbsa = True gbsa_cutoff = 1.100000 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 177 residues in model #52 to IUPAC-IUB standards. > isolde sim start #2.2/D:152 Sim termination reason: None ISOLDE: stopped sim > addh #2.2 Summary of feedback from adding hydrogens to 7b5k-pdb-bundle1.pdb #2.2 --- warnings | Not adding hydrogens to 7b5k-pdb-bundle1.pdb #2.2/A G 1 P because it is missing heavy-atom bond partners Not adding hydrogens to 7b5k-pdb-bundle1.pdb #2.2/B U 1 P because it is missing heavy-atom bond partners Not adding hydrogens to 7b5k-pdb-bundle1.pdb #2.2/W THR 10 CB because it is missing heavy-atom bond partners Not adding hydrogens to 7b5k-pdb-bundle1.pdb #2.2/1 ILE 54 CB because it is missing heavy-atom bond partners notes | No usable SEQRES records for 7b5k-pdb-bundle1.pdb (#2.2) chain 0; guessing termini instead No usable SEQRES records for 7b5k-pdb-bundle1.pdb (#2.2) chain 1; guessing termini instead No usable SEQRES records for 7b5k-pdb-bundle1.pdb (#2.2) chain 2; guessing termini instead No usable SEQRES records for 7b5k-pdb-bundle1.pdb (#2.2) chain 3; guessing termini instead No usable SEQRES records for 7b5k-pdb-bundle1.pdb (#2.2) chain 4; guessing termini instead 26 messages similar to the above omitted Chain-initial residues that are actual N termini: 7b5k-pdb-bundle1.pdb #2.2/0 ALA 2, 7b5k-pdb-bundle1.pdb #2.2/1 GLY 4, 7b5k-pdb-bundle1.pdb #2.2/2 MET 1, 7b5k-pdb-bundle1.pdb #2.2/3 PRO 2, 7b5k-pdb-bundle1.pdb #2.2/4 MET 1, 7b5k-pdb-bundle1.pdb #2.2/5 MET 1, 7b5k-pdb-bundle1.pdb #2.2/C ALA 2, 7b5k-pdb-bundle1.pdb #2.2/D MET 1, 7b5k-pdb-bundle1.pdb #2.2/E MET 1, 7b5k-pdb-bundle1.pdb #2.2/F ALA 2, 7b5k-pdb-bundle1.pdb #2.2/G SER 2, 7b5k-pdb-bundle1.pdb #2.2/H MET 1, 7b5k-pdb-bundle1.pdb #2.2/J MET 1, 7b5k-pdb-bundle1.pdb #2.2/K MET 1, 7b5k-pdb-bundle1.pdb #2.2/L MET 1, 7b5k-pdb-bundle1.pdb #2.2/M MET 1, 7b5k-pdb-bundle1.pdb #2.2/N MET 1, 7b5k-pdb-bundle1.pdb #2.2/O MET 1, 7b5k-pdb-bundle1.pdb #2.2/P SER 2, 7b5k-pdb-bundle1.pdb #2.2/Q ALA 2, 7b5k-pdb-bundle1.pdb #2.2/R MET 1, 7b5k-pdb-bundle1.pdb #2.2/S MET 1, 7b5k-pdb-bundle1.pdb #2.2/T MET 1, 7b5k-pdb-bundle1.pdb #2.2/U ALA 2, 7b5k-pdb-bundle1.pdb #2.2/V MET 1, 7b5k-pdb-bundle1.pdb #2.2/W THR 10, 7b5k-pdb-bundle1.pdb #2.2/X SER 2, 7b5k-pdb-bundle1.pdb #2.2/Y LYS 2, 7b5k-pdb-bundle1.pdb #2.2/Z ALA 2 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: 7b5k-pdb-bundle1.pdb #2.2/0 LYS 57, 7b5k-pdb-bundle1.pdb #2.2/2 LYS 46, 7b5k-pdb-bundle1.pdb #2.2/3 ALA 65, 7b5k-pdb-bundle1.pdb #2.2/4 GLY 38, 7b5k-pdb-bundle1.pdb #2.2/D ALA 209, 7b5k-pdb-bundle1.pdb #2.2/E ALA 201, 7b5k-pdb-bundle1.pdb #2.2/G LYS 177, 7b5k-pdb-bundle1.pdb #2.2/J ILE 142, 7b5k-pdb-bundle1.pdb #2.2/L GLU 144, 7b5k-pdb-bundle1.pdb #2.2/M MET 136, 7b5k-pdb-bundle1.pdb #2.2/O PHE 117, 7b5k-pdb-bundle1.pdb #2.2/P ASN 115, 7b5k-pdb-bundle1.pdb #2.2/Q ALA 118, 7b5k-pdb-bundle1.pdb #2.2/R ALA 103, 7b5k-pdb-bundle1.pdb #2.2/S ARG 110, 7b5k-pdb-bundle1.pdb #2.2/V ALA 94, 7b5k-pdb-bundle1.pdb #2.2/W GLU 85, 7b5k-pdb-bundle1.pdb #2.2/X TYR 78, 7b5k-pdb-bundle1.pdb #2.2/Y ALA 63, 7b5k-pdb-bundle1.pdb #2.2/Z GLU 59 Chain-final residues that are not actual C termini: 7b5k-pdb-bundle1.pdb #2.2/1 ILE 54, 7b5k-pdb-bundle1.pdb #2.2/5 ILE 66, 7b5k-pdb-bundle1.pdb #2.2/C SER 272, 7b5k-pdb-bundle1.pdb #2.2/F ARG 178, 7b5k-pdb-bundle1.pdb #2.2/H GLU 149, 7b5k-pdb-bundle1.pdb #2.2/K LEU 123, 7b5k-pdb-bundle1.pdb #2.2/N ARG 118, 7b5k-pdb-bundle1.pdb #2.2/T LEU 93, 7b5k-pdb-bundle1.pdb #2.2/U ILE 103 11201 hydrogen bonds 7b5k-pdb-bundle1.pdb #2.2/1 ILE 54 is not terminus, removing H atom from 'C' 7b5k-pdb-bundle1.pdb #2.2/5 ILE 66 is not terminus, removing H atom from 'C' 7b5k-pdb-bundle1.pdb #2.2/C SER 272 is not terminus, removing H atom from 'C' 7b5k-pdb-bundle1.pdb #2.2/F ARG 178 is not terminus, removing H atom from 'C' 7b5k-pdb-bundle1.pdb #2.2/H GLU 149 is not terminus, removing H atom from 'C' 4 messages similar to the above omitted 60845 hydrogens added > isolde sim start #2.2/D:149-155 Sim termination reason: None ISOLDE: stopped sim > isolde sim start #2.2/A:747 Sim termination reason: None ISOLDE: stopped sim > isolde sim start #2.2/A:744-750 Sim termination reason: None ISOLDE: stopped sim > hide #2.1 models > show #2.1 models > volume #1 style mesh > volume #1 style surface > volume #1 > transparency #1 50 > addh #2.2 Summary of feedback from adding hydrogens to 7b5k-pdb-bundle1.pdb #2.2 --- warnings | Not adding hydrogens to 7b5k-pdb-bundle1.pdb #2.2/A G 1 P because it is missing heavy-atom bond partners Not adding hydrogens to 7b5k-pdb-bundle1.pdb #2.2/B U 1 P because it is missing heavy-atom bond partners Not adding hydrogens to 7b5k-pdb-bundle1.pdb #2.2/W THR 10 CB because it is missing heavy-atom bond partners Not adding hydrogens to 7b5k-pdb-bundle1.pdb #2.2/1 ILE 54 CB because it is missing heavy-atom bond partners notes | No usable SEQRES records for 7b5k-pdb-bundle1.pdb (#2.2) chain 0; guessing termini instead No usable SEQRES records for 7b5k-pdb-bundle1.pdb (#2.2) chain 1; guessing termini instead No usable SEQRES records for 7b5k-pdb-bundle1.pdb (#2.2) chain 2; guessing termini instead No usable SEQRES records for 7b5k-pdb-bundle1.pdb (#2.2) chain 3; guessing termini instead No usable SEQRES records for 7b5k-pdb-bundle1.pdb (#2.2) chain 4; guessing termini instead 26 messages similar to the above omitted Chain-initial residues that are actual N termini: 7b5k-pdb-bundle1.pdb #2.2/0 ALA 2, 7b5k-pdb-bundle1.pdb #2.2/1 GLY 4, 7b5k-pdb-bundle1.pdb #2.2/2 MET 1, 7b5k-pdb-bundle1.pdb #2.2/3 PRO 2, 7b5k-pdb-bundle1.pdb #2.2/4 MET 1, 7b5k-pdb-bundle1.pdb #2.2/5 MET 1, 7b5k-pdb-bundle1.pdb #2.2/C ALA 2, 7b5k-pdb-bundle1.pdb #2.2/D MET 1, 7b5k-pdb-bundle1.pdb #2.2/E MET 1, 7b5k-pdb-bundle1.pdb #2.2/F ALA 2, 7b5k-pdb-bundle1.pdb #2.2/G SER 2, 7b5k-pdb-bundle1.pdb #2.2/H MET 1, 7b5k-pdb-bundle1.pdb #2.2/J MET 1, 7b5k-pdb-bundle1.pdb #2.2/K MET 1, 7b5k-pdb-bundle1.pdb #2.2/L MET 1, 7b5k-pdb-bundle1.pdb #2.2/M MET 1, 7b5k-pdb-bundle1.pdb #2.2/N MET 1, 7b5k-pdb-bundle1.pdb #2.2/O MET 1, 7b5k-pdb-bundle1.pdb #2.2/P SER 2, 7b5k-pdb-bundle1.pdb #2.2/Q ALA 2, 7b5k-pdb-bundle1.pdb #2.2/R MET 1, 7b5k-pdb-bundle1.pdb #2.2/S MET 1, 7b5k-pdb-bundle1.pdb #2.2/T MET 1, 7b5k-pdb-bundle1.pdb #2.2/U ALA 2, 7b5k-pdb-bundle1.pdb #2.2/V MET 1, 7b5k-pdb-bundle1.pdb #2.2/W THR 10, 7b5k-pdb-bundle1.pdb #2.2/X SER 2, 7b5k-pdb-bundle1.pdb #2.2/Y LYS 2, 7b5k-pdb-bundle1.pdb #2.2/Z ALA 2 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: 7b5k-pdb-bundle1.pdb #2.2/0 LYS 57, 7b5k-pdb-bundle1.pdb #2.2/2 LYS 46, 7b5k-pdb-bundle1.pdb #2.2/3 ALA 65, 7b5k-pdb-bundle1.pdb #2.2/4 GLY 38, 7b5k-pdb-bundle1.pdb #2.2/D ALA 209, 7b5k-pdb-bundle1.pdb #2.2/E ALA 201, 7b5k-pdb-bundle1.pdb #2.2/G LYS 177, 7b5k-pdb-bundle1.pdb #2.2/J ILE 142, 7b5k-pdb-bundle1.pdb #2.2/L GLU 144, 7b5k-pdb-bundle1.pdb #2.2/M MET 136, 7b5k-pdb-bundle1.pdb #2.2/O PHE 117, 7b5k-pdb-bundle1.pdb #2.2/P ASN 115, 7b5k-pdb-bundle1.pdb #2.2/Q ALA 118, 7b5k-pdb-bundle1.pdb #2.2/R ALA 103, 7b5k-pdb-bundle1.pdb #2.2/S ARG 110, 7b5k-pdb-bundle1.pdb #2.2/V ALA 94, 7b5k-pdb-bundle1.pdb #2.2/W GLU 85, 7b5k-pdb-bundle1.pdb #2.2/X TYR 78, 7b5k-pdb-bundle1.pdb #2.2/Y ALA 63, 7b5k-pdb-bundle1.pdb #2.2/Z GLU 59 Chain-final residues that are not actual C termini: 7b5k-pdb-bundle1.pdb #2.2/1 ILE 54, 7b5k-pdb-bundle1.pdb #2.2/5 ILE 66, 7b5k-pdb-bundle1.pdb #2.2/C SER 272, 7b5k-pdb-bundle1.pdb #2.2/F ARG 178, 7b5k-pdb-bundle1.pdb #2.2/H GLU 149, 7b5k-pdb-bundle1.pdb #2.2/K LEU 123, 7b5k-pdb-bundle1.pdb #2.2/N ARG 118, 7b5k-pdb-bundle1.pdb #2.2/T LEU 93, 7b5k-pdb-bundle1.pdb #2.2/U ILE 103 9017 hydrogen bonds 7b5k-pdb-bundle1.pdb #2.2/1 ILE 54 is not terminus, removing H atom from 'C' 7b5k-pdb-bundle1.pdb #2.2/5 ILE 66 is not terminus, removing H atom from 'C' 7b5k-pdb-bundle1.pdb #2.2/C SER 272 is not terminus, removing H atom from 'C' 7b5k-pdb-bundle1.pdb #2.2/F ARG 178 is not terminus, removing H atom from 'C' 7b5k-pdb-bundle1.pdb #2.2/H GLU 149 is not terminus, removing H atom from 'C' 4 messages similar to the above omitted 0 hydrogens added > isolate stepto A 2057 Unknown command: isolate stepto A 2057 > isolate stepto Unknown command: isolate stepto > isolade stepto Unknown command: isolade stepto > isolde stepto > isolde stepto A2057 Unrecognised residue argument! If specified, must be either a residue, "first", "last", "next" or "prev" > isolde stepto A 2057 Expected a keyword > isolde stepto A 981 Expected a keyword > isolde stepto residue A 981 Expected a keyword > isolde stepto residue A981 Unrecognised residue argument! If specified, must be either a residue, "first", "last", "next" or "prev" > isolde stepto residue A:981 Unrecognised residue argument! If specified, must be either a residue, "first", "last", "next" or "prev" > isolde stepto residue Missing "residue" keyword's argument > isolde stepto residue THR:151 Unrecognised residue argument! If specified, must be either a residue, "first", "last", "next" or "prev" > isolde stepto residue THR151 Unrecognised residue argument! If specified, must be either a residue, "first", "last", "next" or "prev" > isolde stepto residue 151 Unrecognised residue argument! If specified, must be either a residue, "first", "last", "next" or "prev" > isolde stepto residue D THR:151 Expected a keyword > isolde stepto residue /D THR:151 Expected a keyword > isolde stepto next > isolde stepto #2.2/D:153 > isolde stepto #2.2/A:2057 > isolde sim start #2.2/A:2057 Sim termination reason: None ISOLDE: stopped sim > hide #!1 models > show #!1 models > volume #1 style mesh > volume #1 style surface > color #1 #55aaff80 models > volume #1 style mesh > volume #1 style surface > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > volume #1 style mesh > ui tool show "Build Structure" QWindowsWindow::setGeometry: Unable to set geometry 1920x1353+0+23 (frame: 1936x1392-8-8) on QWidgetWindow/"MainWindowClassWindow" on "DELL P2422H". Resulting geometry: 1920x1017+0+23 (frame: 1936x1056-8-8) margins: 8, 31, 8, 8 minimum size: 465x1353 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=481, y=1392))) > build start atom #2.2 > isolde stepto #2.2/G:2057 Selection contains no residues! > isolde stepto #2.2/A:2057 > swapna #2.2/A:2057 A Unknown command: isolde swapna #2.2/A:2057 A > swapna Unknown command: isolde swapna > swapna Unknown command: isolde swapna > swapna #2.2/A:2057 A > isolde stepto #2.2/A:2057 > isolde sim start #2.2/A:2057 Sim termination reason: None Traceback (most recent call last): File "C:\Users\jlerath\AppData\Local\UCSF\ChimeraX\1.9\Python311\site- packages\chimerax\isolde\isolde.py", line 876, in start_sim sm = self._sim_manager = SimManager(self, self.selected_model, main_sel, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\jlerath\AppData\Local\UCSF\ChimeraX\1.9\Python311\site- packages\chimerax\isolde\openmm\openmm_interface.py", line 343, in __init__ raise e File "C:\Users\jlerath\AppData\Local\UCSF\ChimeraX\1.9\Python311\site- packages\chimerax\isolde\openmm\openmm_interface.py", line 321, in __init__ sh = self.sim_handler = SimHandler(session, sim_params, sc, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\jlerath\AppData\Local\UCSF\ChimeraX\1.9\Python311\site- packages\chimerax\isolde\openmm\openmm_interface.py", line 1097, in __init__ system = self._system = self._create_openmm_system(ff, top, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\jlerath\AppData\Local\UCSF\ChimeraX\1.9\Python311\site- packages\chimerax\isolde\openmm\openmm_interface.py", line 1230, in _create_openmm_system raise RuntimeError('Unparameterised residue detected') RuntimeError: Unparameterised residue detected During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.9\bin\Lib\site- packages\chimerax\core\triggerset.py", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\jlerath\AppData\Local\UCSF\ChimeraX\1.9\Python311\site- packages\chimerax\isolde\problem_regions\ui.py", line 91, in sim_end_cb self.update() File "C:\Users\jlerath\AppData\Local\UCSF\ChimeraX\1.9\Python311\site- packages\chimerax\isolde\problem_regions\ui.py", line 120, in update clusters, noise = pa.problem_zones(m, restraint_types=restraint_types, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\jlerath\AppData\Local\UCSF\ChimeraX\1.9\Python311\site- packages\chimerax\isolde\problem_regions\problems.py", line 71, in problem_zones sites.extend(vm(structure, outliers_only=validation_outliers_only)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\jlerath\AppData\Local\UCSF\ChimeraX\1.9\Python311\site- packages\chimerax\isolde\problem_regions\problems.py", line 141, in get_protein_backbone_problems problems = f(residues) ^^^^^^^^^^^ File "C:\Users\jlerath\AppData\Local\UCSF\ChimeraX\1.9\Python311\site- packages\chimerax\isolde\molobject.py", line 1057, in non_favored scores, cases = self.validate(residues) ^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\jlerath\AppData\Local\UCSF\ChimeraX\1.9\Python311\site- packages\chimerax\isolde\molobject.py", line 1107, in validate return self._validate_by_residue(residues_or_ramas) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\jlerath\AppData\Local\UCSF\ChimeraX\1.9\Python311\site- packages\chimerax\isolde\molobject.py", line 1124, in _validate_by_residue f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases)) IndexError: No dihedral with that name is registered for this residue type! Error processing trigger "simulation terminated": IndexError: No dihedral with that name is registered for this residue type! File "C:\Users\jlerath\AppData\Local\UCSF\ChimeraX\1.9\Python311\site- packages\chimerax\isolde\molobject.py", line 1124, in _validate_by_residue f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases)) See log for complete Python traceback. ISOLDE: stopped sim OpenGL version: 3.3.14761 Core Profile Forward-Compatible Context 21.30.18.11 30.0.13018.11001 OpenGL renderer: AMD Radeon RX 640 OpenGL vendor: ATI Technologies Inc. Python: 3.11.4 Locale: en_US.cp1252 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: windows Manufacturer: Dell Inc. Model: OptiPlex 7000 OS: Microsoft Windows 10 Enterprise (Build 19045) Memory: 34,033,348,608 MaxProcessMemory: 137,438,953,344 CPU: 20 12th Gen Intel(R) Core(TM) i7-12700 OSLanguage: en-US Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 asttokens: 3.0.0 auditwheel: 6.1.0 autocommand: 2.2.2 babel: 2.16.0 backports.tarfile: 1.2.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2024.8.30 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-Clipper: 0.23.0 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ISOLDE: 1.8.dev0 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 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: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-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: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 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: 1.18.1 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 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: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 comtypes: 1.4.5 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 importlib_metadata: 8.0.0 importlib_resources: 6.4.0 inflect: 7.3.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jaraco.context: 5.3.0 jaraco.functools: 4.0.1 jaraco.text: 3.12.1 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 more-itertools: 10.3.0 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 ordered-set: 4.1.0 packaging: 23.2 packaging: 24.1 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 platformdirs: 4.2.2 prompt_toolkit: 3.0.48 psutil: 6.0.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pywin32: 306 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 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 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4.2 traitlets: 5.14.3 typeguard: 4.3.0 typing_extensions: 4.12.2 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 WMI: 1.5.1 zipp: 3.19.2
Change History (4)
comment:1 by , 9 months ago
Component: | Unassigned → Third Party |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → ISOLDE: Unparameterised residue detected |
comment:2 by , 9 months ago
comment:3 by , 9 months ago
Cc: | added |
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I have noted that for a command with only subcommands, if you issue a subcommand that doesn't exist then the logging drops the main command part. For instance,
build nonesuch 5" logs "nonesuch 5" not "build nonesuch 5" (though the error message that follows does say "Unknown command: build nonesuch 5"). I am going to open a ticket for this. So in this case the user was probably typing "isolde swapna" (except the last time) but only "swapna" was getting logged.
comment:4 by , 9 months ago
Phew. That's much simpler than I feared! :) On Tue, Jan 28, 2025 at 7:03 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote: > > > >
Note:
See TracTickets
for help on using tickets.
The actual traceback here is caused by #14588 (might have to take a day off from my day job to finally tackle that one...). But I'm *really* confused by whatever happened just above:
I don't even know where to start with that... certainly doesn't happen on my machine. Even more confusingly, the last attempt appears to have worked, despite looking identical to the first failed one in the log.