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Opened 10 months ago
Last modified 10 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 , 10 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 , 10 months ago
comment:3 by , 10 months ago
| Cc: | added |
|---|
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 , 10 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.