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#7722 closed defect (nonchimerax)
Maps in sessions with invalid cell angles
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | gregdp@… | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: Linux-4.4.0-201-generic-x86_64-with-glibc2.23
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
I saved this chimeraX session that had the following models:
3 subtomogram average MRC files
2 subtomogram average MRC files with part of the map erased
2 segmentation files
When I open the session, I get this error along with the following in the log:
"/pathToFile/run1.mrc: invalid cell angles 0,0,0 must be between 0 and 180.
/PathToFile/run1_top.mrc: invalid cell angles 0,0,0 must be between 0 and 180.
/PathToFile/run1_bot.mrc: invalid cell angles 0,0,0 must be between 0 and 180."
I'm able to open the above three files, so I'm not to sure where the problem lies. Any help is greatly appreciated!
Best,
Matt
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/ActinModels/Movie/sm2019-09-08-3_tomo8_forVideo.cxs
> format session
Opened temp_chimera_table.em as #1.1, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.2, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.3, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.4, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.5, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.6, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.7, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.8, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.9, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.10, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.11, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.12, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.13, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.14, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.15, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.16, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.17, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.18, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.19, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.20, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.21, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.22, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.23, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.24, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.25, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.26, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.27, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.28, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.29, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.30, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.31, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.32, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.33, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.34, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.35, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.36, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.37, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.38, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.39, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.40, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.41, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.1, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.2, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.3, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.4, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.5, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.6, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.7, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.8, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.9, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.10, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.11, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.12, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.13, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.14, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.15, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.16, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.17, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.18, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.19, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.20, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.21, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.22, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.23, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.24, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.25, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.26, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.27, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.28, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.29, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.30, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.31, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.32, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.33, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.34, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.35, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.36, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.37, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.38, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.39, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.40, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.41, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened TS12_bin4_SL10_noGold.rec as #4, grid size 1023,1440,600, pixel 1,
shown at step 1, values int8
Log from Mon Oct 3 09:55:33 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/ActinModels/sm2019-09-08-3_tomo8.cxs
Opened temp_chimera_table.em as #1.1, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.2, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.3, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.4, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.5, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.6, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.7, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.8, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.9, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.10, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.11, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.12, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.13, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.14, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.15, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.16, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.17, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.18, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.19, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.20, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.21, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.22, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.23, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.24, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.25, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.26, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.27, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.28, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.29, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.30, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.31, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.32, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.33, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.34, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.35, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.36, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.37, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.38, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.39, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.40, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.41, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.1, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.2, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.3, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.4, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.5, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.6, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.7, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.8, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.9, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.10, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.11, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.12, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.13, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.14, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.15, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.16, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.17, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.18, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.19, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.20, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.21, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.22, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.23, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.24, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.25, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.26, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.27, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.28, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.29, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.30, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.31, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.32, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.33, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.34, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.35, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.36, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.37, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.38, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.39, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.40, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.41, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Log from Fri Jul 29 15:23:28 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/ActinModels/sm2019-09-08-3_tomo8.cxs
Opened temp_chimera_table.em as #1.1, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.2, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.3, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.4, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.5, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.6, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.7, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.8, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.9, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.10, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.11, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.12, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.13, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.14, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.15, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.16, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.17, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.18, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.19, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.20, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.21, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.22, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.23, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.24, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.25, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.26, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.27, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.28, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.29, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.30, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.31, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.32, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.33, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.34, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.35, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.36, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.37, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.38, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.39, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.40, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.41, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.1, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.2, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.3, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.4, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.5, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.6, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.7, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.8, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.9, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.10, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.11, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.12, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.13, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.14, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.15, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.16, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.17, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.18, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.19, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.20, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.21, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.22, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.23, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.24, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.25, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.26, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.27, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.28, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.29, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.30, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.31, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.32, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.33, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.34, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.35, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.36, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.37, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.38, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.39, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.40, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.41, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Log from Wed Jul 27 11:32:38 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/ActinModels/sm2019-09-08-3_tomo8.cxs
Opened temp_chimera_table.em as #1.1, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.2, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.3, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.4, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.5, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.6, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.7, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.8, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.9, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.10, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.11, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.12, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.13, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.14, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.15, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.16, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.17, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.18, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.19, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.20, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.21, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.22, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.23, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.24, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.25, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.26, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.27, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.28, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.29, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.30, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.31, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.32, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.33, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.34, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.35, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.36, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.37, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.38, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.39, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.40, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #1.41, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.1, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.2, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.3, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.4, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.5, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.6, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.7, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.8, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.9, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.10, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.11, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.12, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.13, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.14, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.15, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.16, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.17, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.18, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.19, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.20, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.21, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.22, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.23, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.24, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.25, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.26, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.27, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.28, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.29, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.30, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.31, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.32, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.33, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.34, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.35, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.36, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.37, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.38, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.39, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.40, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Opened temp_chimera_table.em as #2.41, grid size 90,90,90, pixel 1, shown at
level 6, step 1, values float32
Log from Wed Jul 27 11:13:09 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open run1_topHalf_Chimera/tomo_1_ChimeraX.cxc
> open
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/temp_chimera_table.em
Opened temp_chimera_table.em as #1.1, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.2, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.3, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.4, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.5, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.6, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.7, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.8, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.9, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.10, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.11, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.12, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.13, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.14, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.15, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.16, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.17, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.18, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.19, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.20, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.21, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.22, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.23, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.24, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.25, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.26, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.27, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.28, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.29, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.30, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.31, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.32, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.33, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.34, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.35, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.36, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.37, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.38, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.39, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.40, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
Opened temp_chimera_table.em as #1.41, grid size 90,90,90, pixel 1, shown at
level 3.84, step 1, values float32
> volume #1.* level 6
> open
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_topHalf_Chimera/tomo_1.positions
> models #1.*.* childModels true
Set 41 positions
> view orient
> color #* #30A6AD
> set bgColor white
executed tomo_1_ChimeraX.cxc
> open
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/tomo_1_ChimeraX.cxc
> open
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/run1_botHalf_Chimera/temp_chimera_table.em
Opened temp_chimera_table.em as #2.1, grid size 90,90,90, pixel 1, shown at
level 1.46, step 1, values float32
Opened temp_chimera_table.em as #2.2, grid size 90,90,90, pixel 1, shown at
level 1.46, step 1, values float32
Opened temp_chimera_table.em as #2.3, grid size 90,90,90, pixel 1, shown at
level 1.46, step 1, values float32
Opened temp_chimera_table.em as #2.4, grid size 90,90,90, pixel 1, shown at
level 1.46, step 1, values float32
Opened temp_chimera_table.em as #2.5, grid size 90,90,90, pixel 1, shown at
level 1.46, step 1, values float32
Opened temp_chimera_table.em as #2.6, grid size 90,90,90, pixel 1, shown at
level 1.46, step 1, values float32
Opened temp_chimera_table.em as #2.7, grid size 90,90,90, pixel 1, shown at
level 1.46, step 1, values float32
Opened temp_chimera_table.em as #2.8, grid size 90,90,90, pixel 1, shown at
level 1.46, step 1, values float32
Opened temp_chimera_table.em as #2.9, grid size 90,90,90, pixel 1, shown at
level 1.46, step 1, values float32
Opened temp_chimera_table.em as #2.10, grid size 90,90,90, pixel 1, shown at
level 1.46, step 1, values float32
Opened temp_chimera_table.em as #2.11, grid size 90,90,90, pixel 1, shown at
level 1.46, step 1, values float32
Opened temp_chimera_table.em as #2.12, grid size 90,90,90, pixel 1, shown at
level 1.46, step 1, values float32
Opened temp_chimera_table.em as #2.13, grid size 90,90,90, pixel 1, shown at
level 1.46, step 1, values float32
Opened temp_chimera_table.em as #2.14, grid size 90,90,90, pixel 1, shown at
level 1.46, step 1, values float32
Opened temp_chimera_table.em as #2.15, grid size 90,90,90, pixel 1, shown at
level 1.46, step 1, values float32
Opened temp_chimera_table.em as #2.16, grid size 90,90,90, pixel 1, shown at
level 1.46, step 1, values float32
Opened temp_chimera_table.em as #2.17, grid size 90,90,90, pixel 1, shown at
level 1.46, step 1, values float32
Opened temp_chimera_table.em as #2.18, grid size 90,90,90, pixel 1, shown at
level 1.46, step 1, values float32
Opened temp_chimera_table.em as #2.19, grid size 90,90,90, pixel 1, shown at
level 1.46, step 1, values float32
Opened temp_chimera_table.em as #2.20, grid size 90,90,90, pixel 1, shown at
level 1.46, step 1, values float32
Opened temp_chimera_table.em as #2.21, grid size 90,90,90, pixel 1, shown at
level 1.46, step 1, values float32
Opened temp_chimera_table.em as #2.22, grid size 90,90,90, pixel 1, shown at
level 1.46, step 1, values float32
Opened temp_chimera_table.em as #2.23, grid size 90,90,90, pixel 1, shown at
level 1.46, step 1, values float32
Opened temp_chimera_table.em as #2.24, grid size 90,90,90, pixel 1, shown at
level 1.46, step 1, values float32
Opened temp_chimera_table.em as #2.25, grid size 90,90,90, pixel 1, shown at
level 1.46, step 1, values float32
Opened temp_chimera_table.em as #2.26, grid size 90,90,90, pixel 1, shown at
level 1.46, step 1, values float32
Opened temp_chimera_table.em as #2.27, grid size 90,90,90, pixel 1, shown at
level 1.46, step 1, values float32
Opened temp_chimera_table.em as #2.28, grid size 90,90,90, pixel 1, shown at
level 1.46, step 1, values float32
Opened temp_chimera_table.em as #2.29, grid size 90,90,90, pixel 1, shown at
level 1.46, step 1, values float32
Opened temp_chimera_table.em as #2.30, grid size 90,90,90, pixel 1, shown at
level 1.46, step 1, values float32
Opened temp_chimera_table.em as #2.31, grid size 90,90,90, pixel 1, shown at
level 1.46, step 1, values float32
Opened temp_chimera_table.em as #2.32, grid size 90,90,90, pixel 1, shown at
level 1.46, step 1, values float32
Opened temp_chimera_table.em as #2.33, grid size 90,90,90, pixel 1, shown at
level 1.46, step 1, values float32
Opened temp_chimera_table.em as #2.34, grid size 90,90,90, pixel 1, shown at
level 1.46, step 1, values float32
Opened temp_chimera_table.em as #2.35, grid size 90,90,90, pixel 1, shown at
level 1.46, step 1, values float32
Opened temp_chimera_table.em as #2.36, grid size 90,90,90, pixel 1, shown at
level 1.46, step 1, values float32
[had to delete a bunch of the log to fit within ticket limits]
> move x 60
> hide #1 #2 #3
> show #4
> volume #4 planes z,280,60,3
> wait 100
> volume #4 planes z,60,280,3
> wait 100
> show #1 #2 #3
> volume #4 planes z,280,60,3
> wait 100
> hide #4
> turn y 2 270
> wait 290
> fly 40 start p1
> wait 80
> wobble y 45 360 cycle 180
> wait 360
> fly 40 p1 p2
> wait 80
> wobble y 45 360 cycle 180
> view name p3
> view p2
> turn y 2 180
> fly 180 p2 p3
> view p2
> turn y 2 180
> view name p4
> view p2
> fly 40 p2 p4
> turn y 2 180
[Repeated 1 time(s)]
> view name p4
> view p2
> fly 40 p2 p4
> wait 40
> turn y 2 180
> view p2
> fly 40 p2 p4
> wait 35
> turn y 2 180
> fly 40 p2 p4
> wait 39
> turn y 2 180
> fly 40 p2 p4
> wait 40
> turn y 2 90
> wait 90
> fly 40 start p3
> fly 40 p2 p4
> wait 40
> turn y 2 90
> wait 90
> fly 40 start p3
> fly 40 p2 p4
> wait 40
> turn y 2 90
> wait 100
> fly 40 start p3
> fly 40 p2 p4
> wait 40
> turn y 2 90
> wait 100
> fly 80 start p3
> Fly 40 p2 p4; wait 40; turn y 2 90; wait 100; fly 80 start p3;
Unknown command: Fly 40 p2 p4; wait 40; turn y 2 90; wait 100; fly 80 start
p3;
> show all
> view orient
> turn z 45
> turn y -15
> zoom 3
> move y -60
> move x 60
> hide #1 #2 #3
> show #4
> volume #4 planes z,280,60,3
> wait 100
> volume #4 planes z,60,280,3
> wait 100
> show #1 #2 #3
> volume #4 planes z,280,60,3
> wait 100
> hide #4
> turn y 2 270
> wait 290
> fly 40 start p1
> wait 80
> wobble y 45 360 cycle 180
> wait 360
> fly 40 p1 p2
> wait 80
> wobble y 45 360 cycle 180
> turn y 2 180
> fly 180 p2 p3
> fly 40 p2 p4
> wait 40
> turn y 2 90
> wait 100
> fly 80 start p3
> stop
> show all
> view orient
> turn z 45
> turn y -15
> zoom 3
> move y -60
> move x 60
> hide #1 #2 #3
> show #4
> volume #4 planes z,280,60,3
> wait 100
> volume #4 planes z,60,280,3
> wait 100
> show #1 #2 #3
> volume #4 planes z,280,60,3
> wait 100
> hide #4
> turn y 2 270
> wait 290
> fly 40 start p1
> wait 80
> wobble y 45 360 cycle 180
> wait 360
> fly 40 p1 p2
> wait 80
> wobble y 45 360 cycle 180
> wait 400
> turn y 2 180
> fly 180 p2 p3
> fly 40 p2 p4
> wait 40
> turn y 2 90
> wait 100
> fly 80 start p3
> VIEW P3
Unknown command: VIEW P3
> view p3
[Repeated 1 time(s)]
> view p4
> fly 40 start p1
> wait 80
> wobble y 45 360 cycle 180
> wait 360
> fly 40 p1 p2
> wait 80
> wobble y 45 360 cycle 180
> wait 400
> turn y 2 180
> fly 180 p2 p3
> fly 40 start p1
> wait 80
> wobble y 45 360 cycle 180
> wait 360
> fly 40 p1 p2
> wait 80
> wobble y 45 360 cycle 180
> wait 400
> fly 40 p2 p4
> wait 40
> turn y 2 90
> wait 100
> fly 80 start p3
> show all
> view orient
> turn z 45
> turn y -15
> zoom 3
> move y -60
> move x 60
> hide #1 #2 #3
> show #4
> volume #4 planes z,280,60,3
> wait 100
> volume #4 planes z,60,280,3
> wait 100
> show #1 #2 #3
> volume #4 planes z,280,60,3
> wait 100
> hide #4
> turn y 2 270
> wait 290
> fly 40 start p1
> wait 80
> wobble y 45 360 cycle 180
> wait 360
> fly 40 p1 p2
> wait 80
> wobble y 45 360 cycle 180
> wait 400
> fly 40 p2 p4
> wait 40
> turn y 2 90
> wait 100
> fly 80 start p3
> view p2
> view p4 40
> view p2 p4 40
Expected an integer >= 1 or a keyword
> view p2
> view p4 40
> view p3 40
> view p4
> fly 40 p4 p3
> view p4
> view p3 80
> show all
> view orient
> turn z 45
> turn y -15
> zoom 3
> move y -60
> move x 60
> hide #1 #2 #3
> show #4
> volume #4 planes z,280,60,3
> wait 100
> volume #4 planes z,60,280,3
> wait 100
> show #1 #2 #3
> volume #4 planes z,280,60,3
> wait 100
> hide #4
> turn y 2 270
> wait 290
> fly 40 start p1
> wait 80
> wobble y 45 360 cycle 180
> wait 360
> fly 40 p1 p2
> wait 80
> wobble y 45 360 cycle 180
> wait 400
> fly 40 p2 p4
> wait 80
> view p3 80
> view p2
> wobble y 30 360 cycle 180
> wait 400
> show all
> view orient
> turn z 45
> turn y -15
> zoom 3
> move y -60
> move x 60
> movie record
> hide #1 #2 #3
> show #4
> volume #4 planes z,280,60,3
> wait 100
> volume #4 planes z,60,280,3
> wait 100
> show #1 #2 #3
> volume #4 planes z,280,60,3
> wait 100
> hide #4
> turn y 2 270
> wait 290
> fly 40 start p1
> wait 80
> wobble y 45 360 cycle 180
> wait 360
> fly 40 p1 p2
> wait 80
> wobble y 30 360 cycle 180
> wait 400
> fly 40 p2 p4
> wait 80
> view p3 80
> movie encode
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/ActinModels/Movie/PCR_F-
> actin_Movie.mov
Movie saved to /ChangLab1-hd2/matt/.../Movie/PCR_F-actin_Movie.mov
> save
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/ActinModels/Movie/sm2019-09-08-3_tomo8_forVideo.cxs
> turn y 2 270
> wait 290
> show all
> view orient
> turn z 45
> turn y -15
> zoom 3
> move y -60
> move x 60
> movie record
> hide #1 #2 #3
> show #4
> volume #4 planes z,280,60,3
> wait 100
> volume #4 planes z,60,280,3
> wait 100
> show #1 #2 #3
> volume #4 planes z,280,60,3
> wait 100
> hide #4
> turn y 3 180
> wait 200
> fly 40 start p1
> wait 80
> wobble y 45 270 cycle 135
> wait 360
> fly 40 p1 p2
> wait 80
> wobble y 30 360 cycle 180
> wait 400
> fly 40 p2 p4
> wait 80
> view p3 80
> wait 100
> movie encode
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/ActinModels/Movie/PCR_F-
> actin_Movie.mov
Movie saved to /ChangLab1-hd2/matt/.../Movie/PCR_F-actin_Movie.mov
> show all
> view orient
> turn z 45
> turn y -15
> zoom 3
> move y -60
> move x 60
> movie record
> hide #1 #2 #3
> show #4
> volume #4 planes z,280,60,3
> wait 100
> volume #4 planes z,60,280,3
> wait 100
> show #1 #2 #3
> volume #4 planes z,280,60,3
> wait 100
> hide #4
> turn y 3 180
> wait 200
> fly 40 start p1
> wait 80
> wobble y 45 180 cycle 90
> wait 180
> fly 40 p1 p2
> wait 80
> wobble y 30 180 cycle 90
> wait 220
> fly 40 p2 p4
> wait 80
> view p3 80
> wait 100
> movie encode
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/ActinModels/Movie/PCR_F-
> actin_Movie.mov
Movie saved to /ChangLab1-hd2/matt/.../Movie/PCR_F-actin_Movie.mov
> save
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/ActinModels/Movie/sm2019-09-08-3_tomo8_forVideo.cxs
——— End of log from Mon Oct 3 09:55:33 2022 ———
opened ChimeraX session
> hide #!1 models
> hide #!2 models
> hide #3 models
> show #!4 models
> show #4.1 models
> volume #4 planes z
> volume #4 planes z depth 5
Expected a keyword
> volume #4 planes z,5
> volume #4 region 0,0,0,1022,1439,599 step 4
> volume #4 region 0,0,0,1022,1439,599 step 4 showOutlineBox true imageMode
> "tilted slab" tiltedSlabAxis 0.02836,-0.1331,0.9907 tiltedSlabOffset 199.2
> tiltedSlabPlaneCount 30
> volume #4 tiltedSlabAxis 0.1809,0.1628,0.9699 tiltedSlabOffset 468.3
> volume #4 region 0,0,0,1022,1439,599 step 1 colorMode opaque8 orthoplanes
> xyz positionPlanes 511,719,299 imageMode orthoplanes
> volume #4 region 0,0,0,1022,1439,599 step 4 maximumIntensityProjection true
> colorMode auto8 imageMode "full region"
> volume #4 region 0,0,296,1022,1439,296 step 1 maximumIntensityProjection
> false
> volume #4 region 0,0,251,1022,1439,251
> volume #4 region 0,0,263,1022,1439,263
> close
> open
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/AlignedAverages/Movie/PCR_average_Movie.cxs
> format session
/ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/AlignedAverages/run1.mrc:
invalid cell angles 0,0,0 must be between 0 and 180.
/ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/AlignedAverages/run1_top.mrc:
invalid cell angles 0,0,0 must be between 0 and 180.
/ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/AlignedAverages/run1_bot.mrc:
invalid cell angles 0,0,0 must be between 0 and 180.
Unable to restore session, resetting.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 725, in restore
obj = sm.restore_snapshot(self, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/segger/regions.py", line 985, in restore_snapshot
sp = r.make_surface()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/segger/regions.py", line 1189, in make_surface
tf.transform_points(vertices, in_place = True)
AttributeError: 'NoneType' object has no attribute 'transform_points'
opened ChimeraX session
> open
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/AlignedAverages/Movie/PCR_average_Movie.cxs
> format session
/ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/AlignedAverages/run1.mrc:
invalid cell angles 0,0,0 must be between 0 and 180.
/ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/AlignedAverages/run1_top.mrc:
invalid cell angles 0,0,0 must be between 0 and 180.
/ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/AlignedAverages/run1_bot.mrc:
invalid cell angles 0,0,0 must be between 0 and 180.
Unable to restore session, resetting.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 725, in restore
obj = sm.restore_snapshot(self, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/segger/regions.py", line 985, in restore_snapshot
sp = r.make_surface()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/segger/regions.py", line 1189, in make_surface
tf.transform_points(vertices, in_place = True)
AttributeError: 'NoneType' object has no attribute 'transform_points'
opened ChimeraX session
> open
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/AlignedAverages/Movie/PCR_average_Movie.cxs
> format session
/ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/AlignedAverages/run1.mrc:
invalid cell angles 0,0,0 must be between 0 and 180.
/ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/AlignedAverages/run1_top.mrc:
invalid cell angles 0,0,0 must be between 0 and 180.
/ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/AlignedAverages/run1_bot.mrc:
invalid cell angles 0,0,0 must be between 0 and 180.
Unable to restore session, resetting.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 725, in restore
obj = sm.restore_snapshot(self, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/segger/regions.py", line 985, in restore_snapshot
sp = r.make_surface()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/segger/regions.py", line 1189, in make_surface
tf.transform_points(vertices, in_place = True)
AttributeError: 'NoneType' object has no attribute 'transform_points'
opened ChimeraX session
> open
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/AlignedAverages/Movie/PCR_average_Movie.txt
Unrecognized file suffix '.txt'
> open
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/AlignedAverages/Movie/PCR_average_Movie.cxs
/ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/AlignedAverages/run1.mrc:
invalid cell angles 0,0,0 must be between 0 and 180.
/ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/AlignedAverages/run1_top.mrc:
invalid cell angles 0,0,0 must be between 0 and 180.
/ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/AlignedAverages/run1_bot.mrc:
invalid cell angles 0,0,0 must be between 0 and 180.
Unable to restore session, resetting.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 725, in restore
obj = sm.restore_snapshot(self, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/segger/regions.py", line 985, in restore_snapshot
sp = r.make_surface()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/segger/regions.py", line 1189, in make_surface
tf.transform_points(vertices, in_place = True)
AttributeError: 'NoneType' object has no attribute 'transform_points'
opened ChimeraX session
> open
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/AlignedAverages/run1.mrc
> format mrc
Summary of feedback from opening
/ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/AlignedAverages/run1.mrc
---
note |
/ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/AlignedAverages/run1.mrc:
invalid cell angles 0,0,0 must be between 0 and 180.
Opened run1.mrc as #1, grid size 360,360,360, pixel 1, shown at level 4.07,
step 2, values float32
> open
> /ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/AlignedAverages/Movie/PCR_average_Movie.cxs
/ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/AlignedAverages/run1.mrc:
invalid cell angles 0,0,0 must be between 0 and 180.
/ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/AlignedAverages/run1_top.mrc:
invalid cell angles 0,0,0 must be between 0 and 180.
/ChangLab1-hd2/matt/Cryptosporidium/ApicalRing/Dynamo_PCR/AlignedAverages/run1_bot.mrc:
invalid cell angles 0,0,0 must be between 0 and 180.
Unable to restore session, resetting.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 725, in restore
obj = sm.restore_snapshot(self, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/segger/regions.py", line 985, in restore_snapshot
sp = r.make_surface()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/segger/regions.py", line 1189, in make_surface
tf.transform_points(vertices, in_place = True)
AttributeError: 'NoneType' object has no attribute 'transform_points'
opened ChimeraX session
OpenGL version: 3.3.0 NVIDIA 384.130
OpenGL renderer: Quadro P4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision 7920 Tower
OS: Ubuntu 16.04 xenial
Architecture: 64bit ELF
Virutal Machine: none
CPU: 24 Intel(R) Xeon(R) Gold 6136 CPU @ 3.00GHz
Cache Size: 25344 KB
Memory:
total used free shared buff/cache available
Mem: 62G 12G 40G 816M 9.7G 48G
Swap: 0B 0B 0B
Graphics:
17:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104GL [Quadro P4000] [10de:1bb1] (rev a1)
Subsystem: Dell Device [1028:11a3]
Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
distro: 1.6.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
line-profiler: 3.3.0
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.3
ParmEd: 3.2.0
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
File attachment: PCR_average_Movie.cxs
Change History (10)
comment:1 by , 3 years ago
comment:2 by , 3 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Maps in sessions with invalid cell angles |
Reported by Matthew Martinez
comment:3 by , 3 years ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
Hi Matt,
MRC files have a header that says what the angles are between xy, yz, and xz axes because in crystallography those angles are not often not 90 degrees. Whatever program wrote your MRC files said those angles are 0 which is invalid and is a bug in the program that wrote the files. You might want to contact the authors of that program so they can fix it. When ChimeraX gets this bad data it tries to carry on by assuming the angles were 90 degrees which is the most common outside of crystallography.
run1.mrc: invalid cell angles 0,0,0 must be between 0 and 180.
Version 0, edited 3 years ago by (next)
follow-up: 4 comment:4 by , 3 years ago
Hi Tom,
Thanks for the quick response. I changed the MRC headers of the 3 files so that the cell angles are 90, however I still get the same error when trying to open the ChimeraX session, just without the error about the cell angles:
"Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/session.py", line 725, in restore
obj = sm.restore_snapshot(self, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 985, in restore_snapshot
sp = r.make_surface()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/segger/regions.py", line 1189, in make_surface
tf.transform_points(vertices, in_place = True)
AttributeError: 'NoneType' object has no attribute 'transform_points'"
This error sounds like it might be due to the segmentation that I'm opening with it, but I've been able to open this segmentation multiple times and in other sessions. Let me know if you think there's any way of restoring this session, or if I should just start from the beginning. Thanks!
Matt
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Tuesday, October 4, 2022 1:49 PM
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; Martinez, Matthew <mpm896@pennmedicine.upenn.edu>
Subject: [External] Re: [ChimeraX] #7722: Maps in sessions with invalid cell angles
#7722: Maps in sessions with invalid cell angles
----------------------------------+-------------------------
Reporter: mpm896@… | Owner: Tom Goddard
Type: defect | Status: closed
Priority: normal | Milestone:
Component: Sessions | Version:
Resolution: nonchimerax | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
----------------------------------+-------------------------
Changes (by Tom Goddard):
* status: assigned => closed
* resolution: => nonchimerax
Comment:
Hi Matt,
MRC files have a header that says what the angles are between xy, yz, and
xz axes because in crystallography those angles are not often not 90
degrees. Whatever program wrote your MRC files said those angles are 0
which is invalid and is a bug in the program that wrote the files. You
might want to contact the authors of that program so they can fix it.
When ChimeraX gets this bad data it tries to carry on by assuming the
angles were 90 degrees which is the most common outside of
crystallography.
run1.mrc: invalid cell angles 0,0,0 must be between 0 and 180.
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7722#comment:3>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
comment:5 by , 3 years ago
| Cc: | added |
|---|
Glad you got the MRC file cell angle problem figured out.
The traceback is an entirely different problem and a bug in Segger. You might try opening the session in ChimeraX 1.4 or better a ChimeraX daily build. You reported the bug for ChimeraX 1.3 and I've made various Segger fixes since then. But I don't think I fixed this one. Segger was developed by Greg Pintilie for Chimera. I ported it to ChimeraX but Greg is still using old Chimera and Segger is 30000 lines of code so I have not been able to fix a lot of the problems. Been hoping the Greg will start using ChimeraX.
At any rate, looking at the Segger code it appears to me that the transform that is None that is causing this problem is because the volume data associated with the segmentation is not being loaded, maybe because the original volume file was not found. The transform that causes the error comes from that volume file and is None when the volume is not available. The code should handle this better so it does not try to use the transform when the volume is not loaded. If you make sure the original volume file is still available where the Segger session file expects to find it then it will probably work without this error.
I see I put a fix in for this problem 7 months ago, so it is in ChimeraX 1.4. But the fix was to make Segger add the needed transform to the session file when it is saved so if it gets restored without the volume it still knows the transform. By the way, the transform goes from the volume i,j,k grid indices to their x,y,z positions (in Angstroms) so usually just encodes the volume grid spacing. So if you saved your Segger session in ChimeraX 1.3, this fix does not help because the session file simply does not have the information if restoring it cannot find the original volume file.
follow-up: 6 comment:6 by , 3 years ago
I've narrowed the error down to somethings related to the segmentation. I'm opening the segmentation of a density map independently of the original density map that was used to segment it. If I save a session with just the segmentation, I always get an error when trying to open the session. If I save a session with just a density map, it opens fine. If I have both a density map and the segmentation, sometimes it won't throw an error when opening the session, but most of the time it will give me an error. Hope this helps.
Matt
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Tuesday, October 4, 2022 2:30 PM
To: Martinez, Matthew <mpm896@pennmedicine.upenn.edu>; goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>
Subject: [External] Re: [ChimeraX] #7722: Maps in sessions with invalid cell angles
#7722: Maps in sessions with invalid cell angles
----------------------------------+-------------------------
Reporter: mpm896@… | Owner: Tom Goddard
Type: defect | Status: closed
Priority: normal | Milestone:
Component: Sessions | Version:
Resolution: nonchimerax | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
----------------------------------+-------------------------
Comment (by mpm896@…):
{{{
Hi Tom,
Thanks for the quick response. I changed the MRC headers of the 3 files so
that the cell angles are 90, however I still get the same error when
trying to open the ChimeraX session, just without the error about the cell
angles:
"Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 725, in restore
obj = sm.restore_snapshot(self, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/segger/regions.py", line 985, in restore_snapshot
sp = r.make_surface()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/segger/regions.py", line 1189, in make_surface
tf.transform_points(vertices, in_place = True)
AttributeError: 'NoneType' object has no attribute 'transform_points'"
This error sounds like it might be due to the segmentation that I'm
opening with it, but I've been able to open this segmentation multiple
times and in other sessions. Let me know if you think there's any way of
restoring this session, or if I should just start from the beginning.
Thanks!
Matt
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Tuesday, October 4, 2022 1:49 PM
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; Martinez, Matthew
<mpm896@pennmedicine.upenn.edu>
Subject: [External] Re: [ChimeraX] #7722: Maps in sessions with invalid
cell angles
#7722: Maps in sessions with invalid cell angles
----------------------------------+-------------------------
Reporter: mpm896@… | Owner: Tom Goddard
Type: defect | Status: closed
Priority: normal | Milestone:
Component: Sessions | Version:
Resolution: nonchimerax | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
----------------------------------+-------------------------
Changes (by Tom Goddard):
* status: assigned => closed
* resolution: => nonchimerax
Comment:
Hi Matt,
MRC files have a header that says what the angles are between xy, yz, and
xz axes because in crystallography those angles are not often not 90
degrees. Whatever program wrote your MRC files said those angles are 0
which is invalid and is a bug in the program that wrote the files. You
might want to contact the authors of that program so they can fix it.
When ChimeraX gets this bad data it tries to carry on by assuming the
angles were 90 degrees which is the most common outside of
crystallography.
run1.mrc: invalid cell angles 0,0,0 must be between 0 and 180.
--
Ticket URL:
<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7722#comment:3>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
}}}
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7722#comment:4>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
follow-up: 7 comment:7 by , 3 years ago
Just read your response as I was writing the previous one. Thanks for this! The computer I'm using only has Ubuntu 16 so I'm unsure if I'll be able to run ChimeraX 1.4. I'll try loading the segger map with the original density map and see if that helps!
Matt
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Tuesday, October 4, 2022 2:55 PM
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; gregdp@gmail.com <gregdp@gmail.com>; Martinez, Matthew <mpm896@pennmedicine.upenn.edu>
Subject: [External] Re: [ChimeraX] #7722: Maps in sessions with invalid cell angles
#7722: Maps in sessions with invalid cell angles
----------------------------------+-------------------------
Reporter: mpm896@… | Owner: Tom Goddard
Type: defect | Status: closed
Priority: normal | Milestone:
Component: Sessions | Version:
Resolution: nonchimerax | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
----------------------------------+-------------------------
Changes (by Tom Goddard):
* cc: gregdp@… (added)
Comment:
Glad you got the MRC file cell angle problem figured out.
The traceback is an entirely different problem and a bug in Segger. You
might try opening the session in ChimeraX 1.4 or better a ChimeraX daily
build. You reported the bug for ChimeraX 1.3 and I've made various Segger
fixes since then. But I don't think I fixed this one. Segger was
developed by Greg Pintilie for Chimera. I ported it to ChimeraX but Greg
is still using old Chimera and Segger is 30000 lines of code so I have not
been able to fix a lot of the problems. Been hoping the Greg will start
using ChimeraX.
At any rate, looking at the Segger code it appears to me that the
transform that is None that is causing this problem is because the volume
data associated with the segmentation is not being loaded, maybe because
the original volume file was found. The transform that causes the error
comes from that volume file and is None when the volume is not available.
The code should handle this better so it does not try to use the transform
when the volume is not loaded. If you make sure the original volume file
is still available where the Segger session file expects to find it then
it will probably work without this error.
I see I put a fix in for this problem 7 months ago, so it is in ChimeraX
1.4. But the fix was to make Segger add the needed transform to the
session file when it is saved so if it gets restored without the volume it
still knows the transform. By the way, the transform goes from the volume
i,j,k grid indices to their x,y,z positions (in Angstroms) so usually just
encodes the volume grid spacing. So if you saved your Segger session in
ChimeraX 1.3, this fix does not help because the session file simply does
not have the information if restoring it cannot find the original volume
file.
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7722#comment:5>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
follow-up: 8 comment:8 by , 3 years ago
I don't think ChimeraX 1.4 runs on Ubuntu 16. Unfortunately the Qt 6 window toolkit ChimeraX uses dropped support for Ubuntu 16 and 18 and so we can only distribute it for Ubuntu 20 and 22. We were surprised they dropped these and CentOS 7 but there is nothing we can do to fix that.
follow-up: 9 comment:9 by , 3 years ago
Yea, we'll have to figure out how to effectively update the OS on these computers. Anyways, I found the original density maps and was able to associate the segmentation with the original density map in the segger dialog box. This seems to have fixed the issue (for now) as the chimeraX session opens after closing it. Thanks again for your help and quick replies!
Matt
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Tuesday, October 4, 2022 3:06 PM
To: Martinez, Matthew <mpm896@pennmedicine.upenn.edu>; goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>
Cc: gregdp@gmail.com <gregdp@gmail.com>
Subject: [External] Re: [ChimeraX] #7722: Maps in sessions with invalid cell angles
#7722: Maps in sessions with invalid cell angles
----------------------------------+-------------------------
Reporter: mpm896@… | Owner: Tom Goddard
Type: defect | Status: closed
Priority: normal | Milestone:
Component: Sessions | Version:
Resolution: nonchimerax | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
----------------------------------+-------------------------
Comment (by goddard@…):
{{{
I don't think ChimeraX 1.4 runs on Ubuntu 16. Unfortunately the Qt 6
window toolkit ChimeraX uses dropped support for Ubuntu 16 and 18 and so
we can only distribute it for Ubuntu 20 and 22. We were surprised they
dropped these and CentOS 7 but there is nothing we can do to fix that.
}}}
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7722#comment:8>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
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File PCR_average_Movie.cxs is larger then allowed attachment size (191207483 > 134217728)