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Opened 4 years ago
Closed 4 years ago
#6092 closed defect (duplicate)
Problem parsing alphafold match command
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Command Line | 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-10-10.0.19042
ChimeraX Version: 1.3.dev202108272307 (2021-08-27 23:07:37 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.3.dev202108272307 (2021-08-27)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "D:\\\AF-1\\\3d class\\\146\\\run_it024_class001.mrc"
Opened run_it024_class001.mrc as #1, grid size 96,96,96, pixel 2.32, shown at
level 0.0529, step 1, values float32
> open "D:/AF-1/3d class/146/run_it024_class002.mrc"
Opened run_it024_class002.mrc as #2, grid size 96,96,96, pixel 2.32, shown at
level 0.0348, step 1, values float32
> open "D:/AF-1/3d class/146/run_it024_class003.mrc"
Opened run_it024_class003.mrc as #3, grid size 96,96,96, pixel 2.32, shown at
level 0.0409, step 1, values float32
> open "D:/AF-1/3d class/146/run_it024_class004.mrc"
Opened run_it024_class004.mrc as #4, grid size 96,96,96, pixel 2.32, shown at
level 0.06, step 1, values float32
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> show #!1 models
> open "D:/AF-1/3d class/146/run_it004_half1_class001.mrc"
Opened run_it004_half1_class001.mrc as #5, grid size 96,96,96, pixel 2.32,
shown at level 0.0422, step 1, values float32
> open "D:/AF-1/3d class/146/run_it004_half2_class001.mrc"
Opened run_it004_half2_class001.mrc as #6, grid size 96,96,96, pixel 2.32,
shown at level 0.0423, step 1, values float32
> hide #!6 models
> hide #!5 models
> hide #5.1 models
> show #!5 models
> show #5.1 models
> open "D:/AF-1/3d class/146/run_class001.mrc"
Opened run_class001.mrc as #7, grid size 96,96,96, pixel 2.32, shown at level
0.0422, step 1, values float32
> hide #!1 models
> hide #!5 models
> close #5#1-4,6-7
> open "D:/AF-1/3d class/152/run_it011_class001.mrc" "D:/AF-1/3d
> class/152/run_it011_class002.mrc" "D:/AF-1/3d
> class/152/run_it011_class003.mrc" "D:/AF-1/3d
> class/152/run_it011_class004.mrc"
Opened run_it011_class001.mrc as #1.1, grid size 96,96,96, pixel 2.32, shown
at level 0.0429, step 1, values float32
Opened run_it011_class002.mrc as #1.2, grid size 96,96,96, pixel 2.32, shown
at level 0.051, step 1, values float32
Opened run_it011_class003.mrc as #1.3, grid size 96,96,96, pixel 2.32, shown
at level 0.0413, step 1, values float32
Opened run_it011_class004.mrc as #1.4, grid size 96,96,96, pixel 2.32, shown
at level 0.0415, step 1, values float32
> open "D:/AF-1/3d class/146/run_it010_class001.mrc" "D:/AF-1/3d
> class/146/run_it010_class002.mrc" "D:/AF-1/3d
> class/146/run_it010_class003.mrc" "D:/AF-1/3d
> class/146/run_it010_class004.mrc"
Opened run_it010_class001.mrc as #2.1, grid size 96,96,96, pixel 2.32, shown
at level 0.0412, step 1, values float32
Opened run_it010_class002.mrc as #2.2, grid size 96,96,96, pixel 2.32, shown
at level 0.0333, step 1, values float32
Opened run_it010_class003.mrc as #2.3, grid size 96,96,96, pixel 2.32, shown
at level 0.0484, step 1, values float32
Opened run_it010_class004.mrc as #2.4, grid size 96,96,96, pixel 2.32, shown
at level 0.056, step 1, values float32
> hide #!1 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> open "D:/AF-1/3d class/146/run_it016_class001.mrc" "D:/AF-1/3d
> class/146/run_it016_class002.mrc" "D:/AF-1/3d
> class/146/run_it016_class003.mrc" "D:/AF-1/3d
> class/146/run_it016_class004.mrc"
Opened run_it016_class001.mrc as #3.1, grid size 96,96,96, pixel 2.32, shown
at level 0.0448, step 1, values float32
Opened run_it016_class002.mrc as #3.2, grid size 96,96,96, pixel 2.32, shown
at level 0.034, step 1, values float32
Opened run_it016_class003.mrc as #3.3, grid size 96,96,96, pixel 2.32, shown
at level 0.0433, step 1, values float32
Opened run_it016_class004.mrc as #3.4, grid size 96,96,96, pixel 2.32, shown
at level 0.058, step 1, values float32
> close #1-2
> open "D:/AF-1/3d class/152/run_it016_class001.mrc" "D:/AF-1/3d
> class/152/run_it016_class002.mrc" "D:/AF-1/3d
> class/152/run_it016_class003.mrc" "D:/AF-1/3d
> class/152/run_it016_class004.mrc"
Opened run_it016_class001.mrc as #1.1, grid size 96,96,96, pixel 2.32, shown
at level 0.0499, step 1, values float32
Opened run_it016_class002.mrc as #1.2, grid size 96,96,96, pixel 2.32, shown
at level 0.0481, step 1, values float32
Opened run_it016_class003.mrc as #1.3, grid size 96,96,96, pixel 2.32, shown
at level 0.0416, step 1, values float32
Opened run_it016_class004.mrc as #1.4, grid size 96,96,96, pixel 2.32, shown
at level 0.0421, step 1, values float32
> hide #!3 models
> show #!3 models
> hide #!1 models
> hide #!1.2 models
> hide #!1.3 models
> hide #!3 models
> hide #!1.4 models
> show #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> hide #!3.2 models
> hide #!3.3 models
> hide #!3.4 models
> show #!3 models
> show #!3.2 models
> show #!3.3 models
> show #!3.4 models
> hide #!3.4 models
> hide #!3.3 models
> hide #!3.2 models
> hide #!1 models
> hide #!3.1 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.1 models
> hide #!3.1 models
> hide #!3 models
> show #!3 models
> show #!3.1 models
> hide #!3.1 models
> hide #!3 models
> show #!3 models
> show #!1 models
> show #!3.1 models
> show #!3.2 models
> show #!3.3 models
> show #!3.4 models
> show #!1.2 models
> show #!1.3 models
> show #!1.4 models
> close #1.3
> close #1,3#1.1-2,4
> open "D:/AF-1/3d class/152/run_it016_class001.mrc" "D:/AF-1/3d
> class/152/run_it016_class002.mrc" "D:/AF-1/3d
> class/152/run_it016_class003.mrc" "D:/AF-1/3d
> class/152/run_it016_class004.mrc"
Opened run_it016_class001.mrc as #1.1, grid size 96,96,96, pixel 2.32, shown
at level 0.0499, step 1, values float32
Opened run_it016_class002.mrc as #1.2, grid size 96,96,96, pixel 2.32, shown
at level 0.0481, step 1, values float32
Opened run_it016_class003.mrc as #1.3, grid size 96,96,96, pixel 2.32, shown
at level 0.0416, step 1, values float32
Opened run_it016_class004.mrc as #1.4, grid size 96,96,96, pixel 2.32, shown
at level 0.0421, step 1, values float32
> hide #!1.2 models
> hide #!1.3 models
> hide #!1.4 models
> open "D:/AF-1/3d class/146/run_it016_class001.mrc" "D:/AF-1/3d
> class/146/run_it016_class002.mrc" "D:/AF-1/3d
> class/146/run_it016_class003.mrc" "D:/AF-1/3d
> class/146/run_it016_class004.mrc"
Opened run_it016_class001.mrc as #2.1, grid size 96,96,96, pixel 2.32, shown
at level 0.0448, step 1, values float32
Opened run_it016_class002.mrc as #2.2, grid size 96,96,96, pixel 2.32, shown
at level 0.034, step 1, values float32
Opened run_it016_class003.mrc as #2.3, grid size 96,96,96, pixel 2.32, shown
at level 0.0433, step 1, values float32
Opened run_it016_class004.mrc as #2.4, grid size 96,96,96, pixel 2.32, shown
at level 0.058, step 1, values float32
> hide #!1.1 models
> hide #!1 models
> hide #!2.4 models
> hide #!2.3 models
> hide #!2.1 models
> hide #!2.2 models
> show #!2.1 models
> hide #!2.1 models
> show #!1.1 models
> show #!1.2 models
> hide #!1.1 models
> hide #!1.2 models
> show #!1.3 models
> hide #!1.3 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.1 models
> hide #!1.1 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2.1 models
> hide #2.1.1 models
> hide #!2 models
> close #1-2
> open "D:/AF-1/3d class/146/run_it017_class001.mrc" "D:/AF-1/3d
> class/146/run_it017_class002.mrc" "D:/AF-1/3d
> class/146/run_it017_class003.mrc" "D:/AF-1/3d
> class/146/run_it017_class004.mrc"
Opened run_it017_class001.mrc as #1.1, grid size 96,96,96, pixel 2.32, shown
at level 0.0453, step 1, values float32
Opened run_it017_class002.mrc as #1.2, grid size 96,96,96, pixel 2.32, shown
at level 0.0342, step 1, values float32
Opened run_it017_class003.mrc as #1.3, grid size 96,96,96, pixel 2.32, shown
at level 0.0427, step 1, values float32
Opened run_it017_class004.mrc as #1.4, grid size 96,96,96, pixel 2.32, shown
at level 0.0583, step 1, values float32
> open "D:/AF-1/3d class/152/run_it017_class001.mrc" "D:/AF-1/3d
> class/152/run_it017_class002.mrc" "D:/AF-1/3d
> class/152/run_it017_class003.mrc" "D:/AF-1/3d
> class/152/run_it017_class004.mrc"
Opened run_it017_class001.mrc as #2.1, grid size 96,96,96, pixel 2.32, shown
at level 0.0523, step 1, values float32
Opened run_it017_class002.mrc as #2.2, grid size 96,96,96, pixel 2.32, shown
at level 0.0475, step 1, values float32
Opened run_it017_class003.mrc as #2.3, grid size 96,96,96, pixel 2.32, shown
at level 0.0415, step 1, values float32
Opened run_it017_class004.mrc as #2.4, grid size 96,96,96, pixel 2.32, shown
at level 0.0421, step 1, values float32
> hide #!1 models
> hide #!2.2 models
> hide #!2.4 models
> hide #!2.3 models
> hide #!2.1 models
> show #!2.2 models
> show #!2.3 models
> show #!2.4 models
> hide #!2.3 models
> hide #!2.2 models
> hide #!2.4 models
> show #!2.1 models
> hide #!2.1 models
> hide #!2 models
> show #!1 models
> hide #!1.2 models
> hide #!1.3 models
> hide #!1.4 models
> close #1-2
> open "D:/AF-1/3d class/152/run_it025_class001.mrc" "D:/AF-1/3d
> class/152/run_it025_class002.mrc" "D:/AF-1/3d
> class/152/run_it025_class003.mrc" "D:/AF-1/3d
> class/152/run_it025_class004.mrc"
Opened run_it025_class001.mrc as #1.1, grid size 96,96,96, pixel 2.32, shown
at level 0.0585, step 1, values float32
Opened run_it025_class002.mrc as #1.2, grid size 96,96,96, pixel 2.32, shown
at level 0.0462, step 1, values float32
Opened run_it025_class003.mrc as #1.3, grid size 96,96,96, pixel 2.32, shown
at level 0.0414, step 1, values float32
Opened run_it025_class004.mrc as #1.4, grid size 96,96,96, pixel 2.32, shown
at level 0.0424, step 1, values float32
> hide #!1.2 models
> hide #!1.3 models
> hide #!1.4 models
> close #1
> open "D:/AF-1/3d class/155/run_it017_class001.mrc" "D:/AF-1/3d
> class/155/run_it017_class002.mrc" "D:/AF-1/3d
> class/155/run_it017_class003.mrc" "D:/AF-1/3d
> class/155/run_it017_class004.mrc"
Opened run_it017_class001.mrc as #1.1, grid size 96,96,96, pixel 2.32, shown
at level 0.0413, step 1, values float32
Opened run_it017_class002.mrc as #1.2, grid size 96,96,96, pixel 2.32, shown
at level 0.0522, step 1, values float32
Opened run_it017_class003.mrc as #1.3, grid size 96,96,96, pixel 2.32, shown
at level 0.0407, step 1, values float32
Opened run_it017_class004.mrc as #1.4, grid size 96,96,96, pixel 2.32, shown
at level 0.0506, step 1, values float32
> hide #!1.2 models
> hide #!1.3 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.1 models
> hide #!1.4 models
> show #!1.3 models
> show #!1.2 models
> hide #!1.3 models
> show #!1.1 models
> hide #!1.2 models
> show #!1.2 models
> show #!1.4 models
> hide #!1 models
> show #!1 models
> hide #!1.1 models
> hide #!1.4 models
> show #!1.3 models
> show #!1.1 models
> hide #!1 models
> hide #!1.1 models
> show #!1 models
> hide #!1.2 models
> show #!1.1 models
> close #1.2
> close
> open "D:/AF-1/3d class/155/run_it025_class001.mrc" "D:/AF-1/3d
> class/155/run_it025_class002.mrc" "D:/AF-1/3d
> class/155/run_it025_class003.mrc" "D:/AF-1/3d
> class/155/run_it025_class004.mrc"
Opened run_it025_class001.mrc as #1.1, grid size 96,96,96, pixel 2.32, shown
at level 0.0412, step 1, values float32
Opened run_it025_class002.mrc as #1.2, grid size 96,96,96, pixel 2.32, shown
at level 0.0602, step 1, values float32
Opened run_it025_class003.mrc as #1.3, grid size 96,96,96, pixel 2.32, shown
at level 0.0418, step 1, values float32
Opened run_it025_class004.mrc as #1.4, grid size 96,96,96, pixel 2.32, shown
at level 0.0582, step 1, values float32
> hide #!1.4 models
> show #!1.4 models
> hide #!1.3 models
> hide #!1.1 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.3 models
> show #!1.1 models
> hide #!1.2 models
> hide #!1.1 models
> show #!1.2 models
> show #!1.4 models
> hide #!1.3 models
> hide #!1 models
> open D:/AF-1/refine/A/run_it012_half1_class001.mrc
> D:/AF-1/refine/A/run_it012_half2_class001.mrc
Opened run_it012_half1_class001.mrc as #2.1, grid size 96,96,96, pixel 2.32,
shown at level 0.0405, step 1, values float32
Opened run_it012_half2_class001.mrc as #2.2, grid size 96,96,96, pixel 2.32,
shown at level 0.0405, step 1, values float32
> open D:/AF-1/refine/A/run_it018_half1_class001.mrc
> D:/AF-1/refine/A/run_it018_half2_class001.mrc
Opened run_it018_half1_class001.mrc as #3.1, grid size 96,96,96, pixel 2.32,
shown at level 0.0413, step 1, values float32
Opened run_it018_half2_class001.mrc as #3.2, grid size 96,96,96, pixel 2.32,
shown at level 0.0412, step 1, values float32
> hide #!3 models
> hide #!2.2 models
> hide #!2.1 models
> hide #!2 models
> hide #!1.4 models
> hide #!1.2 models
> show #!2.1 models
> show #!2.2 models
> hide #!2 models
> show #!3 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!2 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> open D:/AF-1/refine/B/run_it013_half1_class001.mrc
> D:/AF-1/refine/B/run_it013_half2_class001.mrc
Opened run_it013_half1_class001.mrc as #4.1, grid size 96,96,96, pixel 2.32,
shown at level 0.0554, step 1, values float32
Opened run_it013_half2_class001.mrc as #4.2, grid size 96,96,96, pixel 2.32,
shown at level 0.0553, step 1, values float32
> hide #!4.2 models
> hide #!4.1 models
> hide #!4 models
> hide #!3.2 models
> hide #!3.1 models
> hide #!2.2 models
> hide #!3 models
> hide #!2 models
> hide #!2.1 models
> open D:/AF-1/refine/B/run_it013_half1_class001.mrc
> D:/AF-1/refine/B/run_it013_half2_class001.mrc
Opened run_it013_half1_class001.mrc as #5.1, grid size 96,96,96, pixel 2.32,
shown at level 0.0554, step 1, values float32
Opened run_it013_half2_class001.mrc as #5.2, grid size 96,96,96, pixel 2.32,
shown at level 0.0553, step 1, values float32
> open D:/AF-1/refine/B/run_it018_half1_class001.mrc
> D:/AF-1/refine/B/run_it018_half2_class001.mrc
Opened run_it018_half1_class001.mrc as #6.1, grid size 96,96,96, pixel 2.32,
shown at level 0.0568, step 1, values float32
Opened run_it018_half2_class001.mrc as #6.2, grid size 96,96,96, pixel 2.32,
shown at level 0.0567, step 1, values float32
> hide #!5 models
> hide #!6 models
> show #!6 models
> show #!5 models
> hide #!6 models
> hide #!5 models
> show #!5 models
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!5 models
> show #!5 models
> show #!6 models
> close #1-6#1.1-4#2.1-2#3.1-2#4.1-2#5.1-2
> open D:/AF-1/refine/158/run_it001_half1_class001.mrc
> D:/AF-1/refine/158/run_it001_half2_class001.mrc
Opened run_it001_half1_class001.mrc as #1.1, grid size 96,96,96, pixel 2.32,
shown at level 0.101, step 1, values float32
Opened run_it001_half2_class001.mrc as #1.2, grid size 96,96,96, pixel 2.32,
shown at level 0.101, step 1, values float32
> open D:/AF-1/refine/158/run_it002_half1_class001.mrc
> D:/AF-1/refine/158/run_it002_half2_class001.mrc
Opened run_it002_half1_class001.mrc as #2.1, grid size 96,96,96, pixel 2.32,
shown at level 0.063, step 1, values float32
Opened run_it002_half2_class001.mrc as #2.2, grid size 96,96,96, pixel 2.32,
shown at level 0.063, step 1, values float32
> hide #!1 models
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!2 models
> volume #2.1 level 0.05937
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2.2 models
> hide #!2 models
> hide #!1.2 models
> hide #!1.1 models
> hide #!1 models
> show #!2 models
> volume #2.1 level 0.05572
> show #!1.1 models
> hide #!2 models
> volume #2.1 level 0.06606
> show #!2 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> volume #2.1 level 0.06454
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!1.1 models
> open "D:/AF-1/initial model/144/run_it100_class001.mrc"
Opened run_it100_class001.mrc as #3, grid size 96,96,96, pixel 2.32, shown at
level 0.0688, step 1, values float32
> hide #!2 models
> hide #!2.1 models
> hide #!3 models
> close #1-3#1.1-2#2.1-2
> open "D:/AF-1/3d class/ 159/run_it020_class001.mrc" "D:/AF-1/3d class/
> 159/run_it020_class002.mrc" "D:/AF-1/3d class/ 159/run_it020_class003.mrc"
> "D:/AF-1/3d class/ 159/run_it020_class004.mrc"
Opened run_it020_class001.mrc as #1.1, grid size 96,96,96, pixel 2.32, shown
at level 0.0577, step 1, values float32
Opened run_it020_class002.mrc as #1.2, grid size 96,96,96, pixel 2.32, shown
at level 0.0469, step 1, values float32
Opened run_it020_class003.mrc as #1.3, grid size 96,96,96, pixel 2.32, shown
at level 0.0406, step 1, values float32
Opened run_it020_class004.mrc as #1.4, grid size 96,96,96, pixel 2.32, shown
at level 0.0405, step 1, values float32
> hide #!1.2 models
> hide #!1.3 models
> hide #!1.4 models
> show #!1.2 models
> show #!1.3 models
> show #!1.4 models
> hide #!1.4 models
> hide #!1.3 models
> hide #!1.2 models
> open "D:/AF-1/3d class/155/run_it025_class001.mrc" "D:/AF-1/3d
> class/155/run_it025_class002.mrc" "D:/AF-1/3d
> class/155/run_it025_class003.mrc" "D:/AF-1/3d
> class/155/run_it025_class004.mrc"
Opened run_it025_class001.mrc as #2.1, grid size 96,96,96, pixel 2.32, shown
at level 0.0412, step 1, values float32
Opened run_it025_class002.mrc as #2.2, grid size 96,96,96, pixel 2.32, shown
at level 0.0602, step 1, values float32
Opened run_it025_class003.mrc as #2.3, grid size 96,96,96, pixel 2.32, shown
at level 0.0418, step 1, values float32
Opened run_it025_class004.mrc as #2.4, grid size 96,96,96, pixel 2.32, shown
at level 0.0582, step 1, values float32
> hide #2.2.1 models
> show #2.2.1 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.3 models
> hide #!2.1 models
> hide #!2 models
> hide #!2.4 models
> show #!2 models
> hide #!2.2 models
> hide #!1.1 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.4 models
> hide #!2.4 models
> show #!1.1 models
> hide #!1.1 models
> show #!2.2 models
> show #!2.3 models
> show #!2.4 models
> show #!2.1 models
> hide #!2.1 models
> hide #!2 models
> show #!1.4 models
> show #!1.3 models
> show #!1.2 models
> hide #!1.2 models
> hide #!1.3 models
> show #!1.1 models
> hide #!1.4 models
> ui tool show AlphaFold
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3.dev202108272307\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 179, in _fetch
self._run_command('match')
File "C:\Program Files\ChimeraX 1.3.dev202108272307\bin\lib\site-
packages\chimerax\alphafold\panel.py", line 204, in _run_command
run(self.session, cmd)
File "C:\Program Files\ChimeraX 1.3.dev202108272307\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.3.dev202108272307\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2812, in run
prev_annos = self._process_positional_arguments()
File "C:\Program Files\ChimeraX 1.3.dev202108272307\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2588, in
_process_positional_arguments
value, text = self._parse_arg(anno, text, session, False)
File "C:\Program Files\ChimeraX 1.3.dev202108272307\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2447, in _parse_arg
value, replacement, rest = annotation.parse(text, session)
File "C:\Program Files\ChimeraX 1.3.dev202108272307\bin\lib\site-
packages\chimerax\atomic\args.py", line 141, in parse
elif is_uniprot_id(text):
File "C:\Program Files\ChimeraX 1.3.dev202108272307\bin\lib\site-
packages\chimerax\atomic\args.py", line 179, in is_uniprot_id
id, text, rest = next_token(text)
File "C:\Program Files\ChimeraX 1.3.dev202108272307\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 1774, in next_token
assert text and not text[0].isspace()
AssertionError
AssertionError
File "C:\Program Files\ChimeraX 1.3.dev202108272307\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 1774, in next_token
assert text and not text[0].isspace()
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 462.30
OpenGL renderer: GeForce GTX 1650 Ti with Max-Q Design/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: LENOVO
Model: 20V3
OS: Microsoft Windows 10 Pro (Build 19042)
Memory: 34,220,064,768
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i7-10870H CPU @ 2.20GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
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: 2021.5.30
cftime: 1.5.0
chardet: 4.0.0
ChimeraX-AddCharge: 1.1.4
ChimeraX-AddH: 2.1.10
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.29
ChimeraX-AtomicLibrary: 4.1.3
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: 2.5.3
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.4
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3.dev202108272307
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.4
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: 2.1.1
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-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: 2.0.1
ChimeraX-MDcrds: 2.5
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.1
ChimeraX-ModelPanel: 1.1
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
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
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
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
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: 2.4.2
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
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: 1.11.1
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
comtypes: 1.1.10
cxservices: 1.0.1
cycler: 0.10.0
Cython: 0.29.23
decorator: 5.0.9
distlib: 0.3.1
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.4.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.20
imagecodecs: 2021.4.28
imagesize: 1.2.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 2.11.3
jupyter-client: 6.1.12
jupyter-core: 4.7.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 1.1.1
matplotlib: 3.4.2
matplotlib-inline: 0.1.2
msgpack: 1.0.2
netCDF4: 1.5.6
networkx: 2.6.2
numexpr: 2.7.3
numpy: 1.21.0
numpydoc: 1.1.0
openvr: 1.16.801
packaging: 21.0
ParmEd: 3.2.0
parso: 0.8.2
pickleshare: 0.7.5
Pillow: 8.2.0
pip: 21.1.1
pkginfo: 1.7.0
prompt-toolkit: 3.0.20
psutil: 5.8.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.9.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pywin32: 228
pyzmq: 22.2.1
qtconsole: 5.1.0
QtPy: 1.10.0
RandomWords: 0.3.0
requests: 2.25.1
scipy: 1.6.3
Send2Trash: 1.8.0
SEQCROW: 1.3
setuptools: 57.0.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.1.0
sortedcontainers: 2.4.0
Sphinx: 4.0.1
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: 5.0.5
urllib3: 1.26.6
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.2
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (2)
comment:1 by , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Command Line |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Problem parsing alphafold match command |
comment:2 by , 4 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Fixed 5 months ago. #5186